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The

telePresence
Add-in

MORADA Camera
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About this document
This document describes the procedure for installing the Morada
system on a TEM column.
It includes the following:
• the installation of hardware components on the PC running your
image analysis program;
• the installation of the Morada camera unit on your microscope's
wide angle port;
• the pneumatic components required for controlling the camera
position;
• the water cooling system's components;
• cabling;
• proper set up of the camera for regular use;
• some handling and usage precautions;
• some servicing information;
• and some technical data.
Please read these instructions before performing an installation.
Some parts or procedures may differ for different models of micro-
scope, but this should not cause any major problems.
Morada User´s Guide Controlling the Morada via software 4

ACQUIRING IMAGES ...............................................................4


DEFINING OFFSET AND GAIN CORRECTION ......................6
ACQUIRING IMAGES WITH INTELLIGENT EXPOSURE ......14
CALIBRATING INPUT CHANNEL ..........................................17
USING RTFFT .........................................................................19
ACTIVATING REMOTE CONTROL ........................................22
USING MACROS IN THE INPUT CHANNEL .........................22
THE CAMERA CONTROL DIALOG BOX ...............................24
CONFIGURING THE INPUT CHANNEL .................................28

Quick-start Installation 37

Handling and Usage Precautions 38

Camera Installation Procedure 41

Software-Installation 53

TROUBLESHOOTING ............................................................66
Morada0407E

Service Notes 69

ADJUSTING THE MORADA IN/OUT MOVEMENT SPEED ...69


ADJUSTING THE PRISM POSITION .....................................70
FOCUSING THE CAMERA ..................................................... 70

Appendix 74

TECHNICAL SPECIFICATIONS ............................................. 74


PACKING LIST ....................................................................... 74
CE DECLARATION ................................................................. 75
WEEE DECLARATION ........................................................... 76
Morada • Controlling the Morada via software

Morada

Controlling the Morada via software


Your image analysis software uses the concept of logical input channels for
the acquisition of images. A logical input channel contains the configuration
of the device being used, as well as other settings for the acquisition and
pre-processing of images.
Only one input channel can be active at any given time. The name of this
active channel is displayed in the status bar.

Acquiring images
Two input channels suitable for the Morada camera will be installed during
the software installation. Use the pre-defined input channel "Morada
11MPixel" when you carry out the step-by-step-instructions that follow.
How a new input channel is created and configured is described on page 28.

Selecting the input channel


1) Switch on your TEM and the Morada control box.
2) Move the camera into the TEM column.
3) Start your image analysis program.
" If the control box has not been correctly connected, the WaaCtrl
dialog box will open.
4) Check the connection, then select the respective serial port, usually
COM 2. Click OK.
4

5) Select the Image > Set Input... command.


" The Set Input dialog box will be opened. It shows the input channels
that are predefined for your Morada camera.
The Set Input dialog box
contains two predefined
channels. These are named
"Morada 11 MPixel" and
"Morada 2k x 2k"
Acquiring images

6) Select the "Morada 11 MPixel" input channel.


" The "Morada 11 MPixel" input channel uses all of the camera area,
and therefore gives you the maximum possible image resolution.

Acquiring images
Switching to the 7) Click the Acquire button located in the Standard button bar.
live mode " The camera’s live-image will be displayed in the image window.
" The online histogram window will be opened. The diagram shows
the current intensity distribution of the live-image.
Online histogram

" Your image analysis program automatically activates the next


image buffer.
8) Select the Image > Camera Control... command.
" The Camera Control dialog box will be opened.
9) Change the exposure time, if necessary. Click the Auto button in the
Camera Control dialog box to have the exposure time be calculated
automatically.
Camera Control

5
10) Locate the sample position you are interested in.
Focusing the 11) Click the Set ROI for Partial readout button located in the Camera
image Control dialog box.
" A red rectangular frame will appear in the live-image.
• Should this not be the case, please activate the Live-Overlay check box
located in the Image > Configure Input > Display tab.
12) To move this frame within the image, move your mouse.
" Look for an image segment containing sample structures with
whose help you can focus the image.
13) Click the right mouse button to confirm the position of the ROI.
Morada • Defining offset and gain correction

14) Click the Partial Readout On/Off button located in the Camera Control
dialog box. The button must appear depressed. In this case, the "partial
readout" mode is activated.
" In "partial readout" mode, only the selected image section is
displayed in the image window, which increases the live-image's
frame rate considerably.
15) Focus the image.
16) Click the Partial Readout On/Off button located in the Camera Control
dialog box once again to deactivate the "partial readout" mode.
Acquiring an 17) Click the Snapshot button located in the Standard button bar.
image " The live-image will be stopped.
• Note that you can directly use the Snapshot button to acquire an image
while you are in the "partial readout" mode. In other words, it is not nec-
essary to switch off the "partial readout" mode to be able to activate the
Snapshot button.
Saving an image 18) Use the File > Save As... command to save the image file, or insert the
image into an image database. You should use the TIF file format in
order to save all additional image information.

Defining offset and gain correction


Shading correction is required for the acquisition of best quality images. Two
reference images (one offset image and one gain image) are required for
each format used in the input channels for the purpose of automatic shading
correction. In fact, you will mainly use the shading correction in the snapshot
mode, i.e., at high resolution, since shading correction reduces the speed in
the live mode.
Offset image A camera offset image is acquired without any illumination. When you use a
CCD camera, you will have to make an offset correction to compensate for
the dark-current signal's inhomogeneity. When a shading correction is
made, the offset image is subtracted from the original image.
To be precise, two offset images with varying exposure times are acquired
and saved. When necessary, a third offset image is then computed for the
current exposure time, from these two offset images. If you alter exposure
6

time, and then acquire an image using online shading correction, the requi-
site offset image will be automatically recomputed without notice.

Related Topics
Focusing the camera . 70
Defining offset and gain correction

A typical Morada offset


image (this image has been
contrast enhanced).
Although the structures
resulting from the inhomo-
geneous dark-current signal
are barely visible, they can -
especially where acquisi-
tions with low-intensity are
concerned - lead to images
that are difficult to analyze.

Gain image The camera gain image is acquired at homogeneous illumination - without
any sample. The camera image is divided by the gain image during shading
correction.
A typical Morada gain
image.
The non-homogeneous illu-
mination of the image field is
readily visible.

7
Online shading correc- With the Online shading correction, your image analysis program corrects
tion fixed image structures (resulting from the imaging system) during acquisi-
tion.
Possible reasons for • Irregular illumination on the CCD chip can, e.g., lead to a dip in intensity
shading at image borders. This results in the borders of the image being darker
than the center.
• The amplification of the signal of individual camera-array pixels can
fluctuate slightly in CCD cameras. Individual pixels are thus somewhat
brighter or darker than neighboring pixels which were illuminated with
exactly the same intensity. This phenomenon can be particularly dis-
turbing when you work with long exposure times.
• Luminescent screen thickness in the prism can vary slightly, resulting
in fluctuations in light yield.
Morada • Defining offset and gain correction

What does shading The following image operations are executed during a real-time shading
correction involve? correction:
1) The offset image is subtracted from the original image.
2) The resulting image will then be divided by the gain image. The gain
image has already been corrected, i.e., the relevant offset image has
already been subtracted from the gain image.
3) The resulting corrected image will then be multiplied by the mean gray
value of the gain image. Mean image brightness is thus not affected by
shading correction.
Shading correction To be able to use the shading correction you must have a valid offset image
prerequisites and a valid gain image. You acquire these reference images with the Image
> Acquire Reference Images... command. When you begin image acquisi-
tion, and your image analysis program cannot find any valid reference
images, you’ll be prompted to acquire reference images.

How to acquire reference images


A wizard guides you through the entire reference images acquisition. It will
enable you to acquire both offset and gain images. Simply follow the
onscreen instructions, select the relevant entries and alter the microscope´s
settings accordingly.
Note that you can only acquire a gain image if a valid offset image is already
available.
The reference images will automatically be saved to the PC´s hard disk.
Warning! • The validity of gain images depend, among other things, on the accel-
eration voltage that has been set on your TEM. If your image analysis
program can directly read out the acceleration voltage set on your TEM
via remote, you will only need to make reference images once for the
necessary acceleration voltage. The correct images will then always be
automatically loaded.
• If you do not have remote control, you will have to acquire a new gain
image whenever you alter the voltage level.
• You will require reference images for every image format. Image for-
mats are defined in the input channel.
8

Acquiring offset 1) Switch on your TEM and the Morada control box.
images 2) Make sure that no light can reach the camera's CCD chip. To do this,
cover up the window of the TEM projection chamber and turn off the
electron beam or close the column valves. Move the camera into the
TEM column.
3) In the Set Input dialog box, select the input channel with which you
want to acquire reference images, e.g., the predefined "Morada
11MPixel" channel.
4) Select the Image > Acquire Reference Images... command to acquire
the offset image.
" The Acquire Reference Images dialog box will be opened.

Related Topics
The Format tab . 34
Defining offset and gain correction

The Acquire Reference


Images dialog box, at Step
1: Selection of the images

5) Should you only want to acquire reference images for the active reso-
lution, select the Acquire for the current camera resolution only option.
6) Click the Next > button.
" The Acquire Reference Images dialog box, shows Step 2: Darken
the camera
The Acquire Reference
Images dialog box, at Step
2: Darken the camera

" You will be asked to set the microscope in such a way that no light
illuminates the camera.
7) Then press Next >.
" The Acquire Reference Images dialog box, shows Step 3:
Acquiring offset images.
Morada • Defining offset and gain correction

The Acquire Reference


Images dialog box, at Step
3: Acquisition of the offset
images

" The offset images needed will be acquired.


" As soon as the procedure is finished, the Acquire gain images
dialog box appears.
" You’ll be asked to remove the sample and to check for homoge-
nous illumination.
8) Do so, then press Next >.
" A live acquisition will then be automatically started, and the Camera
Control dialog box will be opened.
" The Acquire Reference Images dialog box now shows Step 4: Illu-
mination of the camera
The Acquire Reference
Images dialog box, at Step
4: Illumination of the camera
10

9) Click the Select area button, to set a rectangular image segment. The
mean intensity of this area will later be used to increase the brightness
of the images in line with the shading correction.
" Please note: the camera will then run in binning 8. Adjust the illumi-
nation on the TEM so that the exposure time of the camera will be
Defining offset and gain correction

between 25 and 40 ms and the mean gray value of the histogram


is around 50%.
10) Set a homogeneous illumination. The image on your monitor should
now be evenly illuminated. Click the Next > button.
" The gain images will be acquired and saved offset corrected.
The Acquire Reference
Images dialog box, at Step
5: Acquisition of the gain
images

" When the acquisition has been completed, the Acquire reference
images, Step 6: Activation of the correction will be opened.
The Acquire Reference
Images dialog box, at Step
6: Activation of the correc-
tion

11

" The shading correction will then be automatically activated.


11) Click the Finish button to complete the acquisition of the reference
images.
" From now on, all of the images you acquire via the current input
channel will be shading-corrected.
" Please note that you can deactivate, and later reactivate, the online
shading correction, by using the Image > Configure Input > Input
command.
Morada • Defining offset and gain correction

Switching the shading correction on and off


1) Select the Image > Configure Input... command and activate the Input
tab.
Activating the shading
correction in the Configure
Input dialog box.

2) Select the Shading correction > Offset check box, and either the
Shading correction > Gain (Time optimized) check box, or the (Quality
optimized) check box (siehe Seite 29).
3) Click on OK.
" From now on, the altered settings will be valid for all of the images
you acquire with the active input channel.

How to adjust the exposure time


1) Select the Image > Configure Input... command.
12

2) In the Configure Input dialog box, select the Display tab and select the
Online histogram check box.
3) Close the Configure Input dialog box.
4) Use the Image > Camera Control... command.
" The Camera Control dialog box will be opened.
" Check the exposure time. It should be about the same as you are
acquiring your images with.
Adjusting exposure time.
Defining offset and gain correction

5) Select the Image > Acquire command to switch over to the live mode.
" The live-image is displayed in the image window.
" The online histogram window will be opened. The diagram shows
the current intensity distribution of the live-image.
6) Use the histogram to check whether the gray values are situated
centrally in the diagram. As necessary you can alter, e.g., electron
beam intensity or spot size of the electron microscope, and/or adjust
the exposure time a little to shift intensities roughly into the middle of
the graph.
" The mean value shown should be between 40 % and 60 %.
The mean value should be
between 40 % and 60 %.

7) Check, if the mean value still lies between 40 % and 60 %. Then press
OK. Otherwise, alter the electron beam intensity and/or the exposure
time, to arrive at the gray value distribution you want. Then press OK.

How to check reference images


1) Set electron beam intensity at medium brightness.
" Generally, after having acquired reference images correctly, you
will not need to adjust current brightness. During the subsequent
image acquisition, the online histogram should display a mean
value between 40 % and 60 %.
2) Acquire an image - without sample - using the Image > Acquire or
Snapshot command.
" The corrected acquisition should not have any visible structures
13
due to the imaging system. The only thing you should be able to see
is homogeneous noise.
An image acquired without a
sample. If the shading
correction was successful,
the image will show homo-
geneous static noise. This
noise is caused by the elec-
trons’ quantum noise.
The image has been
contrast enhanced.

3) Make sure that the focus is correct before acquiring reference images.
Morada • Acquiring images with Intelligent Exposure

Acquiring images with Intelligent Exposure


Intelligent The Intelligent Exposure acquisition process makes it very easy for you to
Exposure make high-grade acquisitions.

Image resolution: A considerable advantage of using Intelligent Exposure is that you can
acquisition and snap- select different resolutions for the live-image (acquisition) and for the snap-
shots shot. A lower image resolution is suggested by default for the live-image
since the frame rate is then higher and thus the movements in the live-image
are not choppy. If you have a snapshot in your image buffer, it is, however,
recommended that you select the highest camera resolution possible, in
order to obtain the optimal image quality.
Intelligent Exposure enables you to automatize the acquisition process to a
large extent. The exposure times for live-images and snapshots are opti-
mized independently of each other. The optimization of the exposure time
occurs continually and automatically.
XY-calibration and Intelligent Exposure uses the calibration data of the active input channel for
Intelligent Exposure the XY-calibration of the images.
1) Select the Images > Intelligent Exposure... command.
" The Intelligent Exposure dialog box will be opened. When using this
dialog box, you still retain access to all of your image analysis
program's other functions.
2) Click the Acquisition button to start the live image.
" The exposure times calculated by Intelligent Exposure are
displayed in the dialog box's status bar. The term Live Exp. stands
for the exposure time of the live mode, while Snap Exp. stands for
the calculated exposure time of the snapshot.
3) Click the Online histogram On/Off button in the Standard button bar to
switch on the online histogram.
" The histogram shows you if the image is illuminated properly. The
distribution is cut off to the right if the image is over exposed. If the
image is under exposed, the distribution shows a peak at the left.
4) Click the Snapshot button to acquire a single image.
" Intelligent Exposure acquires a snapshot and writes it into the
14

active image buffer. A message box informing you about the acqui-
sition process appears if the exposure time of a snapshot exceeds
one second.

The Intelligent Exposure dialog box


Click the left mouse button to start the live image. Click the right mouse
button to end the live image and to write the image into the image buffer.
Press the [Esc] key to terminate the live mode. Alternatively, you can click
anew on the left button, located in the Intelligent Exposure dialog box.

Related Topics
Focusing the camera . 70
The Intelligent Exposure dialog box

Intelligent Exposure offers a


convenient alternative to the
acquisition commands
Image > Acquire and Image
> Snapshot... ..

Acquisition Click the Acquire button to start the live mode using Intelligent Exposure.
The live image is displayed in the image window. With the help of the live
image you can focus the sample position for the snapshot acquisition.
Characteristics of the live When you use Intelligent Exposure, the speed of the live image has absolute
image priority. For this reason the live image's frame rate will automatically be
increased. This alteration will not affect the snapshots that are made with
Intelligent Exposure.
Snapshot Click the Snapshot button to initiate the acquisition of a snapshot. Should
the snapshot's exposure time exceed one second, a message box will
appear to inform you about the acquisition's progress.
Exposure adjustment The Exposure adjustment slide control enables you to manually influence
the exposure time for snapshots calculated by Intelligent Exposure. Position
’0’ on the slide control does not influence the exposure time which was auto-
matically calculated by Intelligent Exposure. Move the Exposure adjustment
control to the right in order to increase the exposure time. This correction will
cause exactly the same adaptation of the exposure times for both live mode
and snapshot. Only when the exposure time exceeds 125 ms will it be fixed
at this value for live images.
Resetting the Exposure Double click on ’0’ below the Exposure adjustment slide control in order to

15
adjustment use the automatically calculated exposure time values once again.
Focus mode Click the Focus mode button if you want to focus the camera using the
highest image resolution together with the "partial readout" mode.
To enable focusing at the highest resolution, only a small image area is read
out of the camera in the Intelligent Exposure mode. The read out is speeded
up to such an extent that the live-image directly responds to any focus
change. The size of the image area is 512x512. The area position is
predefined. The binning is automatically set to 1, so that the entire resolution
can be used in the selected area. The button is only available in the live
image.
Set ROI for Click the Set ROI for histogram calculation button to define a rectangular
histogram area in the image. The online histogram and the automatic gain display will
only be calculated within this region of interest.
Move the ROI's frame shown in the image window to the desired position.
Set its size by moving the mouse while keeping the left mouse button
depressed. Rightclick to confirm position and size of the ROI.
Related Topics
Partial Readout . 27
Morada • Acquiring images with Intelligent Exposure

Automatic gain display The Intelligent Exposure always uses the automatic gain display to have the
image optimally displayed onscreen independent of the actual illumination
conditions. The system will assess the current intensity histogram in real
time in order to find the optimal onscreen display of the live image.
The automatic gain display affects monitor display only - it does not alter
actual image information.
When the automatic gain display is active, image intensity, as far as monitor
display is concerned, will always be adjusted according to the histogram's
minimum and maximum values. Click the Reduce Contrast or Increase
Contrast button to change the maximum value. The higher the maximum
value, the lower the contrast will be.
Options Click the Options button to set the options for Intelligent Exposure. The Intel-
ligent Exposure Options dialog box will be opened.
The Intelligent Exposure
Options dialog box

Dynamic limit in % Set the dynamic range in which Intelligent Exposure works with the Dynamic
limit in % slide control. Move the slider to the right to increase the dynamic
limit. This setting results in lighter images with a higher contrast in darker
areas of the image. Move the slider to the left to decrease the dynamic limit.
16

This setting results in darker images with better contrast in light areas of the
image.
Max. exposure in s Set the highest exposure time for snapshots by using the Max. exposure in
s slide control. This value limits the maximum exposure time Intelligent
Exposure can use for snapshots. Should Intelligent Exposure calculate a
higher exposure time than determined by Max. Exposure in s, a warning will
appear and the images will be underexposed.
Max. exposure focus Set the highest exposure time in the focus mode by using the Max. exposure
mode in ms focus mode ms slide control. This value defines the maximum exposure time
Intelligent Exposure can use for live image acquisitions in the focus mode.
A warning will appear should this value be exceeded by the current illumina-
tion conditions.
Binning Select the image resolution in the Binning group. Usually you will use 1 x 1
binning for snapshots and a higher binning value in the live-image.
Keep live after snap- Select the Keep live after snapshot check box, to have the live mode resume
shot after you have acquired a snapshot. The snapshot will be written to the
current image buffer. In the next image buffer that has been defined in the
sequence, a new live mode will be started. The Keep live after snapshot
Calibrating input channel

check box is only available if you have selected an entry other than None in
the Sequence list located in the Special > Preferences > Image > Image
acquisition dialog box.
Switching off the live Press the [Esc] key to terminate the live mode. Alternatively you can click
mode anew on the Acquire button located in the Intelligent Exposure dialog box.
Real time FFT Select the Real time FFT check box to have not only the live-image shown
in the live mode, but the continually-updated fourier image shown as well.
This will simplify the adjustment and focusing of the TEM.
Online histogram Select the Online histogram check box to be able to keep an eye on the
intensity distribution during image acquisition. During image acquisition, a
window showing the histogram will appear automatically. This histogram will
be updated continually.
Sharpness monitor for Select the Sharpness monitor for focus mode check box to use the sharp-
focus mode ness monitor as a focusing aid when working in the focus mode. Click the
Focus mode button in the Intelligent Exposure dialog box to activate the
focus mode.

Calibrating input channel


Calibration should be done for every input channel that is used to make
image snapshots.
1) Insert a calibration standard into your microscope. This is normally a
grid or grating with regular known intervals (e.g. a grid with 2160 lines/
mm or 463 nm line spacing).
2) Select the Image > Set Input command. Select the input channel you
want to calibrate.
3) Set a reasonable microscope magnification.
4) Use the Image > Acquire command to optimize the acquisition param-
eters of the calibration standard.
5) Select the Image > Configure Input... command and activate the XY
Calibration tab.

17

Related Topics
Using RTFFT . 19
Sharpness Monitor . 26
Morada • Calibrating input channel

You calibrate the input


channel here.

6) Enter the magnification level that has been set, in the Magnification
field.
7) Enter the length you want to calibrate with, in the Calibration length
field.
8) Click the Unit... button.
" Select m (for meters) in the Basic unit list in the Set Unit dialog box.
" Select, e.g., n in the Scale list if you wish the calibration length to
be nm.
9) Select the Arbitrary option in the Calibration group.
10) Leave the X/Y ratio for the Morada camera at 1.
11) Click the Calibrate button.
" The mouse cursor appears in the image.
" Position the mouse cursor at the starting point of the calibration
18

length and leftclick.


" Then position the mouse cursor at the final point of the calibration
length and confirm by leftclicking. The line must be exactly as long
as the calibration length you entered.
12) Click the Save... button to open a list of calibration data for various
magnifications.
13) Click the Add button to add the data you’ve just calculated to the magni-
fication list and have it included in the diagram as well.
14) If the list in the Magnification Table dialog box initially included invalid
calibration data, then select these entries and click the Delete button.
Using RTFFT

This is where you check the


calibration.

15) Exit this dialog box by clicking on OK.


16) Repeat these steps for other magnifications to obtain a magnification
calibration curve.
• To do so, you don’t have to leave the Configure Input dialog box. Alter
the microscope magnification. Click the Acquire button in the Configure
Input dialog box, and use the live-image to position and focus the cali-
bration standard. When you’re satisfied, quit the live mode by clicking
on Snapshot. Now you can repeat the calibration on that image.
17) When you have performed all of the calibrations, click the OK button to
confirm this.
Note When you have calibrated an existing channel, you can adopt this calibra-
tion for new channels too. To do so, select the Image > Set Input...
command. Activate the existing channel whose calibration data you want to
adopt. Press the New channel button. In the Select device dialog box,

19
choose the Morada entry. Select the Use calibration of active channel check
box and confirm via OK.

Using RTFFT
The Real-time Fast Fourier Transformation (RTFFT) is a tremendous
help when interactively adjusting the electron beam in the TEM and when
focusing the image. In the live mode, besides having the live-image shown,
you can have the continually-updated fourier image (the absolute value of
its fourier transform):
Morada • Using RTFFT

The fourier image of a 2-D


catalase crystal.
The light spots represent the
periodic structures in the
microscope image. The
closer such a spot is located
to the center of the fourier
image, the lesser the local
frequency of the corre-
sponding periodic structure -
i.e., the greater the periodic
distances within the image.
(The luminous ‘cross’ is a
result of a fringe effect.)

Adjustment and When you are working with thin, amorphous specimens, circular structures
focusing using RTFFT will become visible in the RTFFT image. Should these structures have an
elliptical form, this indicates an astigmatism. If this astigmatism is corrected
in the TEM, the ellipses within the fourier image will become circular in
shape.
Two fourier images of an
amorphous specimen.
The elliptical shape of the
structures in the left image
indicates an astigmatism.
The astigmatism has been
corrected in the right image:
the ellipses have become
circular.
20

If the acquired image becomes out of focus, the high local frequencies - i.e.,
the structures located further away from the center - will disappear.
If you’ve switched on a Wobbler on your TEM that rapidly flips the electron
beam back and forth, fringes may appear within the fourier image. These
fringes indicate that the electron beam is not precisely focused on the spec-
imen. When you focus the beam, the distance between the fringes will
increase and the fringes will then move out of the image.
Using RTFFT

Microscope image and


corresponding fourier image
of latex beads.
Two partial images overlap
one another in the micro-
scope image (left) because
the (not- precisely-focused)
electron beam is being
flipped back and forth by the
Wobbler.
This is why a fringe pattern
occurs in the fourier image
(right).

Activating RTFFT The RTFFT function with the RTFFT Display window and the RTFFT Control
dialog boxes is activated by selecting the Real time FFT check box in the
Image > Configure Input > Display tab.
Alternatively, click the RTFFT On/Off button located in the Standard button
bar to activate the display of the real time FFT.

The RTFFT Control dialog box


Use the RTFFT Control dialog box to improve onscreen display of the fourier
image:

21
ROI tab On the ROI tab define the size (256x256 or 512x512) and the position of the
(centered) image segment (Region Of Interest) used to compute the fourier
image.
Select the Show ROI check box, to have a red frame displayed. To change
the position of this frame, move your mouse. While depressing the left
mouse button, move your mouse, to alter the size of the frame. The right
mouse button enables you to set the frame.
Visualization tab On the Visualization tab use the scroll bars to adjust contrast and bright-
ness.
Tools tab On the Tools tab, select the 90°Rotation check box to tilt the image 90°
clockwise. This may be necessary - depending on the flange (the latter
depending on the microscope) - to obtain an image whose orientation
matches that on the fluorescence screen.
Select the Overlay Circle check box to display a circle in the overlay of the
fourier image. The center of the circle is the origin of the fourier image. The
slide control enables you to manually modify its radius.
Morada • Activating remote control

Click the Grab FFT button to create an identical copy of the fourier image as
a gray value image with 8-bit-depth of data. This image will be written into
the destination image buffer of your image analysis program.

Activating remote control


Most microscopes have remote control capabilities that will allow your image
analysis program to read the current magnification of the microscope via a
serial cable connection. This ensures that all images acquired will carry the
correct calibration information assuming that the microscope or input
channel is properly calibrated.
1) Select the Image > Configure Input... command and activate the
Magnification tab.
This is where you activate
the remote control.
22

2) The name of the microscope should be displayed in the Device list.


Select this device.
3) Select the Remote > On check box.
4) Try to get a magnification reading by clicking the Read button.
" Magnification is automatically read via the remote control, every
time a snapshot is made.

Using macros in the input channel


You can specify macros in the input channel that will be automatically
performed before, and/or, after the image acquisition. Two examples of
macros will be shown in the following section.

Setting the magnification


If your microscope cannot be operated by remote control, you must specify
the magnification. This macro will request you to specify the magnification
after every image.
Using macros in the input channel

1) Select the Image > Configure Input... command and activate the Macro
tab.
2) Type in the function SetMagnification$() in the Postprocessing steps
field. Put a semicolon at the end of the line.
" This command will open the Set Magnification dialog box after each
image acquisition.
3) Test the little macro. To do so, click the Execute button.
• If you receive an error message, check your spelling of the command.
• If the Set Magnification dialog box opens, your macro functions correct-
ly.
This is where you enter the
macro command.

4) Click the OK button to confirm the new configuration of the input


channel.
5) Click the Snapshot button located in the Standard button bar.

23
" The Set Magnification dialog box will be opened. Enter the micro-
scope magnification and confirm via OK.

Moving the prism into the microscope automatically


By using this macro, you will determine that the prism is moved into the light
path before the acquisition is made, and out of it after the acquisition has
been made.
1) Type in the function WaaCtrl::CamIn() in the Preprocessing steps field.
Put a semicolon at the end of the line.
" Now the prism will automatically be moved into the light path before
the acquisition is made.
2) Type in the function WaaCtrl::CamOut() in the Postprocessing steps
field. Put a semicolon at the end of the line.
" Now the prism will automatically be moved out of the light path after
the acquisition is made.
Morada • The Camera Control dialog box

The Camera Control dialog box


The Image > Camera Control command and the appropriate dialog box
enables you to attain control over numerous setting possibilities required for
acquiring single images and live images. The commands in this dialog box
are closely interlocked with the settings in the Configure Input dialog box.
The Camera Control command is only available if the Set Input dialog box
is closed.
The Camera Control dialog
box for a Morada camera

Exposure Time
Exposure You can set the camera's exposure time in the Exposure time group.
Click the [-] and [+] buttons to alter the exposure time in pseudo-logarithmic
steps. You can also directly change the exposure time in the corresponding
text field or manipulate it using the arrow buttons next to the text field. The
minimum and maximum exposure times depend on the camera being used.
Auto To have the exposure time automatically set, click the Auto button. The Auto
button is only available in live-mode.
Please note, that you may not see the effect of a higher exposure time on
the image displayed in the image window if you use the automatic display
function. In this case you should use the online histogram to check your
exposure time. If the online histogram has been shifted to intensity values
that are too high, this may result in an overexposure of some image areas.

Automatic Gain Display and Fixed Scaling


24

The Morada camera acquires images with an intensity range of 14-bit. This
means that an image can comprise intensity values ranging from 0 - 16383.
However, only 8 bits, i.e. 0-255 values can be used for the display. For this
reason, the original intensity values have to be shown in the range of 0-255.
Let’s take the following example. If the minimum intensity value of the orig-
inal image is 0 and the maximum intensity value is 2550, the following
mapping function is one possible way of displaying the intensity values on
your monitor. All intensity values 0-9 are displayed using the intensity value
0. All intensity values 9-19 are displayed using the intensity value 1, and so
forth.
Keep in mind that only the monitor display will be changed, not the actual
image intensity. When measuring image intensities you will always get the
’real’ image intensity, not the image intensity that is displayed on the
monitor.
However, there are several different mapping functions that can be used for
displaying the image on your monitor.

Related Topics
Configuring the input channel . 28
The Camera Control dialog box

Fixed scaling The "Fixed scaling" method uses a fixed intensity range that is used to
display all images on the monitor. Only the intensity values that are within
this range will be shown on your monitor. The limits for this fixed intensity
range can either be manually set or automatically calculated from the inten-
sity histogram. Use this method, e.g., if you want to compare the brightness
of different images.
Automatic gain display The "Automatic gain display" method extracts the intensity range that is
displayed, based on the actual signals on hand. Use this method, e.g., to be
sure to see something on the monitor, even if an image is actually underex-
posed.
Use automatic Click the Use automatic gain display button to activate the automatic gain
gain display display. Then the live-image will always be displayed on your monitor with
optimal contrast, regardless of the illumination conditions. The behavior of
the "automatic gain display" depends on how the overflow for this function
has been set, and on which area of the image the contrast enhancement is
calculated. You can set the overflow you want by using the Image >
Configure Input command, located on the Display tab. The following possi-
bilities for selecting the image area can be found in the Camera Control
dialog box.
Please note, that the following methods for calculating the histogram affect
the automatic gain display and the histogram that is shown in the online
histogram.
Histogram Click the Histogram calculation on full image button to carry out the contrast
calculation on optimization on the basis of the entire image. This option is recommended if
full image the structures to be observed are equally dispersed throughout the entire
image.
Histogram Click the Histogram calculation on crosshair button, to only take the pixels
calculation on along a strip which is only a few pixels wide in the horizontal and vertical
crosshair direction, into consideration.
Histogram Click the Histogram calculation on ROI button, to carry out the contrast opti-
calculation on mization on the basis of a rectangular area within the image. You can use
ROI this option when relevant details are only visible in one segment of the
image. This enables you to optimize the display for just this segment.

25
Set ROI for Click the Set ROI for histogram button to interactively set the rectangular
histogram area of the image for optimizing the contrast. This button is only available if
the Histogram calculation on ROI button is depressed. To change the posi-
tion of this frame, move your mouse. To alter the size of the frame, while
keeping the left mouse button depressed, move your mouse. Press the right
mouse button to finish the frame setting process.
Use fixed Click the Use fixed scaling button to use the "fixed scaling" method. The
scaling limits for this fixed intensity range can either be manually set or automati-
cally calculated from the intensity histogram. For example, if the limits are 0
- 3825, all intensity values 0-14 are displayed using the intensity value 0. All
intensity values 15-30 are displayed using the intensity value 1, and so forth.
All intensity values greater than 3825 are set to 255.
The mapping function will be used for all images, and will not be automati-
cally adjusted if the intensity range of the image changes. When using the
fixed scaling, the image will no longer be optimally displayed when the illu-
mination or sample are altered.
Automatically Click the Automatically adjust fixed scaling button to have the scaling auto-
adjust fixed matically set under the current conditions. This button is only available in the
scaling live mode.
Morada • The Camera Control dialog box

Manually Click the Manually adjust fixed scaling button, if you want to set the limits for
adjust fixed the fixed scaling manually. The Fixed scaling dialog box will be opened.
scaling
The Fixed scaling dialog
box.

Move the Left limit and Right limit slide controls, or enter the desired numer-
ical value directly in the text field.

Sharpness Monitor
The Sharpness Monitor allows you to control the focus settings in the live
mode. You can define a rectangular area in the image that is to be analyzed
for the sharpness monitor. The maximum contrast serves as a monitor for
the sharpness in this area. For this reason, you should take care that the
area of the image that is to be used for the sharpness monitor is one with
plenty of contrast.
The live overlay must be activated for the sharpness monitor. This can be
done via the Display tab, located in the Configure Input dialog box.
What the sharpness The Sharpness Monitor consists of a dialog box in which a relative measure-
monitor is for ment of the sharpness is displayed by a changing bar which can be varied
between Blurred and Focused.
The Sharpness Monitor

If you start the live mode with an activated Sharpness Monitor or activate it
during the live mode, its bar will initially show middle sharpness (50%). This
is because there is no absolute measurement for the sharpness in an image
26

and because the sharpness monitor only delivers relative values, which
relate to the initial situation at the time the live mode was started.
Focusing and Sharpness If you alter the focus settings when you are in the live mode with an activated
Monitor sharpness monitor, the length of the bar will change. In doing so, the green
marker bar shows the maximum sharpness reached since the live mode
was started. Should the sharpness increase due to your changes, the bar
will correspondingly shift to the right. If the focus settings are already optimal
when you start an acquisition, the bar can only shift towards Blurred.
Reset to 90% Click the Reset to 90% button to set the sharpness monitor's relative value
to 90%. Use this function if you start working with a very blurry image, which
causes the sharpness monitor's bar to already reach the right hand limit
while you are focusing. By resetting to 90%, you give the display more room
for additional focusing. The Reset to 90% function is also useful if the sharp-
ness drops very drastically due to changes made to the microscope settings
while an acquisition is in progress.

Related Topics
The Display tab . 31
The Camera Control dialog box

This is how you set the sharpness monitor to make good acqui-
sitions
1) Set all other parameters (microscope settings, exposure time) opti-
mally. The application of the sharpness monitor should be the last step
before image acquisition.
2) Acquire a snapshot.
3) Use the Image > Camera Control... command.
4) Click the Set ROI for sharpness monitor button to interactively define a
rectangular area of the image for the sharpness monitor.
" To do this, select an area of the specimen for which a good sharp-
ness setting is especially important.
5) Start a live image.
" The Set ROI for sharpness monitor button becomes inactive.
6) Click the sharpness monitor on/off button to open the sharpness
monitor dialog box.
" The sharpness monitor begins with a value of 50%.
7) Vary the focus settings and observe the sharpness monitor while doing
so.
" The sharpness monitor bar shows the current sharpness, the blue
marker shows the highest achieved sharpness.
" You must watch the exposure time while you are setting the focus.
When you use longer exposure times, (> 100 ms) the sharpness
monitor's reaction time will increase. Vary the focus settings in
small intervals, and between them until the sharpness monitor has
reacted.
8) Find the focus settings by which the sharpness monitor is at its
maximum and use these settings for the acquisition.

Partial Readout
The "partial readout" mode is a method for achieving fast live images. A rect-
angular part of the image, to which the readout is limited during live-mode,
is defined for the "partial readout" mode. Due to the smaller amount of data
that is transferred, a higher frame rate is attained.

27
The live overlay must be activated for the "partial readout" mode. This can
be done via the Display tab, located in the Configure Input dialog box.
Partial Readout and Clip- The "partial readout" mode and clipping functions both lead to smaller
ping images than those acquired without these functions. The "partial readout"
mode already works when the image is read out of the camera; The image
areas which are faded out by this function are not transferred to the PC. The
clipping, however, is calculated out of the complete image data in the PC.
This, therefore, does not result in an acceleration in the image acquisition.
Owing to the camera's very high pixel count, the frame rate, when full reso-
lution is used, is often not enough to enable good focusing in the live-mode.
In order to attain both high resolution and high frame rates, you must do the
following:
1) Start the live-image using full resolution.
2) Set the ROI for the "partial readout" mode on an important image detail.
3) Activate the "partial readout" mode.

Related Topics
The Display tab . 31
Morada • Configuring the input channel

4) Make the required settings.


5) Deactivate the "partial readout" mode.
" Should the "partial readout" mode be activated, the image area set
will also apply to the following snapshot.
6) Acquire a snapshot.
Partial Readout Click the Partial Readout On/Off button. Instead of the camera's entire CCD
on/off chip, now only a rectangular area which was defined with the Set ROI for
Partial Readout function, is read out. Should you activate the "partial
readout" mode before a ROI has been set for this function, a predefined ROI
is used in the image center.
Please note that the image resolution is not changed in the "partial readout"
mode. A snapshot that you acquire in this mode will not only show the
defined image segment, it will show the complete image.
Set ROI for Click the Set ROI for Partial Readout button to interactively set the rectan-
Partial Readout gular area of the image to be read out. Pull the ROI's red frame, shown in
the image window, to a position on the image which is to be read out.
Change the size of the area by keeping the mouse button depressed and
moving the pointer. Rightclick to confirm position and size of the ROI. The
Set ROI for Partial Readout command does not enable the partial readout;
you still have to click the Partial Readout On/Off button afterwards.

Configuring the input channel


Duplicating already existing input
Do not change the predefined input channels. If you want to configure the
input channel differently, first duplicate one of the already existing channels.
By doing so, you retain all of the input channel's settings.
1) Select the Image > Set Input... command.
" All current logical input channels are listed in the Set Input dialog
box.
2) Select one of the existing input channels, for example the Morada 11
MPixel input channel.
28

3) Click the Duplicate channel button.


" The selected input channel will be copied together with its settings,
and a new input channel will be created with these settings. The
number 1 will be added to the name of the input.

Configuring inputs
1) Select the Image > Set Input... command. Select an already existing
input.
2) Click the Configure Input button to define the properties of this input
channel.
" The Configure Input dialog box will be opened.
The Configure Input dialog box

The Configure Input dialog box


The Configure Input dialog box contains several tabs for setting the proper-
ties of input channels. The tabs Input, Display and Format contained in this
dialog box are described in the following. These three tabs contain the
specific settings that apply to the Morada.
Viewing channel data When you acquire an image via a Morada input channel, its properties will
automatically be saved along with the image. This data can be viewed at a
later point in time. To do so, load the image into an image buffer and double-
click on that image buffer in the image manager. The Image Information
dialog box will be opened. Channel properties are recorded in the Channel
Data tab.

The Input tab

Exposure time Enter the number of microseconds the camera's CCD chip is to be exposed, 29
in the Exposure field. You can also set the value in this field while viewing
the live image, with the aid of the Camera Control dialog box.
Shading correction Use the Shading correction group to have rigid image structures corrected
during image acquisition - these structures may result from, e.g., an irregular
illumination of the image field.
Select the Offset check box to have the offset image subtracted during
image acquisition.
Select one or both Gain check boxes to have the image divided by the gain
image during image acquisition.
Time optimized In the basic setting for the online shading correction, the Gain (Time opti-
mized) check box is selected. With this setting, the gain images will be
adopted without any change, exactly as they were acquired.

Related Topics
The Camera Control dialog box . 24
Defining offset and gain correction . 6
Morada • Configuring the input channel

Quality optimized The mechanical tolerances in the prism's drive system can lead to a shifting
of the gain images in comparison to the actual acquisition. In this case it is
possible that despite valid gain images, structures will once more become
visible in the image, these will have been caused by the copying system.
Select the Gain (Quality optimized) check box, to have this effect automati-
cally compensated. The calculations that this makes necessary will lengthen
the acquisition process.
Trigger Mode Use a trigger when you want the start of the image acquisition to be delayed
until your PC receives a signal from another device. For example, this could
be a beam blanker that prevents the sample from being damaged during a
kryo-application process, .
In the basic setting, the no Trigger option is selected. In this case you will
actuate the acquisition by using the Image > Acquire command.
You can select between two possible trigger signals.
If you choose the Trigger In option from the Trigger Mode list, a default TTL
signal of 5 V is expected.
Use the Trigger Out Level option, to set an active trigger signal during the
acquisition. The trigger signal will be active during the whole exposure time.
Note You should only then select another entry than No Trigger, if there really is
a trigger signal. The following entries Trigger In and Trigger Out Level block
the acquisition process. The system then waits for a signal. You can inter-
rupt this by pressing [Esc].
Rotation The image orientation on the TEM fluorescence screen may not match that
of the camera image displayed on your monitor. If you want the images on
the monitor to be oriented the same way as on the screen, you will have to
set the correct rotation value. Enter a suitable angle value in the Rotation
field.
Select the correct rotation angle from the Rotation list, to have the camera
image oriented the same way as on the TEM fluorescence screen. The rota-
tion (0°, 90° or 270° rotation) will be performed as selected.
Note If you change the rotation, the reference images are no longer valid and
must be reacquired.
30

In the case of a 270° rotation the camera image is shown edgewise. Such a
representation is not advantageous, as the image can only be completely
displayed when a very small zoom factor is used. Decide what is more
important for you: a favorable representation on the monitor, or the same
orientation on the fluorescence screen as on your monitor.
Click the Info... button to view information on the device in use in the Morada
Camera Information dialog box:

Related Topics
How to acquire reference images . 8
The Configure Input dialog box

The Morada Camera Infor-


mation dialog box

Temperature The CCD Chip field indicates the temperature measured directly on the CCD
chip. The operating temperature is 15°C.

The Display tab

31

Over exposure The Over exposure group is where you determine when, or if, an overexpo-
sure warning is to appear. Using the intensity histogram, your image anal-
ysis program continually checks image intensity in the live mode and will
warn you as soon as the live image becomes too bright.
Morada • Configuring the input channel

Select the Display warning check box to activate the overexposure warning.

An image is overexposed when a certain percentage of all pixels have


reached the maximum possible intensity value. You enter this percentage in
the Overflow field.
Automatic gain display Use the functions of the Automatic gain display group, to have the image
optimally displayed onscreen regardless of the actual illumination condi-
tions. The system will assess the current intensity histogram in real time in
order to find the optimal onscreen display of the live image.
The "automatic gain display" method affects monitor display only - it does
not alter actual image information.
Select the Activate check box to turn on the automatic gain display.
When the automatic gain display is active, image intensity as far as monitor
display is concerned, will be spread between the minimum and maximum
values of the online histogram. You determine these values in the Left over-
flow and Right overflow fields. Enter the percentage of pixels with the lowest
intensity values which are to be displayed black, and which percentage of
the highest intensity values are to be displayed white.
In this way you can clip intensity values that are to be ignored at both the
upper and lower ends of the histogram. Make use of the overflow values to
prevent individual outlier pixels or minute image areas that are too bright or
too dark, from influencing the automatic gain display.
Fixed scaling Instead of using the automatic gain display, you can use the fixed scaling.
The group whose Activate check box has been selected will be the one
available - the other will not be available.
You select definite limits for the intensity range that you wish to have opti-
mally spread for onscreen display. Any intensity value occurring outside of
this defined intensity range will appear either black or white. Enter the
minimum intensity limit in the Left limit field - the maximum intensity limit in
the Right limit field.
32

The "fixed scaling" method affects monitor display only - it does not alter
actual image information.
Online histogram Select the Online histogram check box to be able to keep an eye on the
intensity distribution during image acquisition.
Alternatively, click the Online histogram On/Off button located in the Stan-
dard button bar to switch on the online histogram.

The histogram is calculated either on the full image, along a crosshair, or on


a user-defined ROI (Region of Interest). Use the buttons in the Camera
Control dialog box to choose which histogram calculation you want to use.
The Configure Input dialog box

Beneath the histogram, minimum, mean and maximum gray values of the
image will be shown. Percentages are in relation to the maximum obtainable
intensity value.
When working with the Morada (with its 14-bit depth), the maximum obtain-
able intensity value is 16384. This intensity value corresponds to 100%. A
mean of 85% would thus correspond to an intensity value of 13926.
Please note that you can also switch between the automatic display and the
fixed scaling, in the Histogram dialog box. To activate one display mode, just
click the corresponding button.
Show histogram ROI Select the Show histogram ROI check box to display the ROI used for calcu-
lating the histogram in the live mode. This check box is available only if the
live overlay has been activated. Please note that this setting is only relevant
if you have selected the Histogram Calculation on ROI option in the Camera
Control dialog box. By default, the histogram is calculated on the cross hair.
To select another ROI, use the Set ROI for histogram button in the Camera
Control dialog box
Real time FFT Select the Real time FFT check box to have not only the live-image shown
in the live mode, but also the fourier image, that will be continually updated.
This will simplify the adjustment and focusing of the TEM.
Live overlay Select the Live overlay check box if you want to use overlays in live-images.
The live overlay is absolutely essential for both the "Partial Readout" and the
"Real time FFT" modes.
The Live overlay check box is only available if your display board features a

33
so-called hardware overlay which is supported by Microsoft DirectX. Almost
any up-to-date AGP display board provides you with that feature. You can
look at the System Info dialog box to check whether your display board
offers this feature. To do so, select the Info... command, located in the ?
menu and click the System Info button. The System Info dialog box will be
opened. Click the "DirectX" entry in the list on the left-hand side, to have the
desired information appear in the list on the right-hand side.
Fixed zoom for binning If you modify the binning, the pixel resolution changes. This means that the
image displayed in your image window, will change its size. Select the Fixed
zoom for binning check box, to have the image on your monitor always
displayed in the same size, regardless of the current binning settings.
By default, the zoom factor for the live-image is set at 100% when a 4x4
binning is active. If you select another binning, the zoom factor will be
adjusted to keep the image size unchanged.

Related Topics
Using RTFFT . 19
Morada • Configuring the input channel

Image scaling In the Image scaling list, select one of the four possibilities for displaying an
image in the image window.
Select the Underscan entry to have the whole image displayed. The system
will select the largest zoom level - 25%, 50% or 100% - at which the whole
image can still be displayed in the image window. In certain cases the image
window will not be used fully.
Select the Overscan entry to ensure that all the image window’s available
area will be used. The system will select the smallest zoom level - 25%, 50%
or 100% - at which the image fills the whole image window. In certain cases,
the image will not be completely displayed.
Select the Adjust to viewport entry to have the image size adjusted to opti-
mally fit the image window. The image will be adjusted to fit the current size
of the image window.
Select the Full size (100%) entry to have the image displayed without any
zooming at all. If the image window is smaller than the image, as much of
the image will be shown as fits - starting from the upper left-hand corner of
the image.

The Format tab


34

Image format The Image format list contains a series of predefined standard image
formats:
• 4008 x 2672 Pixel, Binning 1 x 1
• 2004 x 1336 Pixel, Binning 2 x 2
• 1002 x 668 Pixel, Binning 4 x 4
• 500 x 334 Pixel, Binning 8 x 8
The very first time you call up this tab, the Morada's maximum obtainable
resolution will have been preset. With this setting, images will not be clipped.
In addition, this list contains user-defined image formats. You can define
your own image formats in the Clipping border (pixel) group. User-defined
image formats are denoted by the appearance of the word "free" along with
The Configure Input dialog box

the entry - e.g., "free, 450 x 334 Pixel, Binning 8 x 8". You may select either
a predefined, or a user-defined, image format, from the list. The format you
select will be the one set the next time you call up this tab.
A graphic display of the clipped areas can be seen in the Active area field.
The values are shown in the fields of the Clipping border (pixel) group.
Binning is when the camera integrates the contents of neighboring pixels.
This will result in a more speedy read-out and greater sensitivity - image
resolution will however decrease.
Use binning when you, e.g., are working with an electron microscope at low
intensities, because binning will reduce noise. Binning can also be useful if
a rapid frame rate is of greater priority than a high image resolution.
Horizontal Enter the number of neighboring pixels to be integrated, in the Horizontal
Vertical and Vertical fields.
You cannot alter the values in the Horizontal and Vertical fields indepen-
dently of each other. If you alter one value, the other will automatically be
adjusted accordingly.
Clipping border (pixel) Define the number of lines and columns that are to be clipped from the
edges, in the Clipping border (pixel) group. The corresponding format will be
indicated in the Image format field and displayed graphically in the Active
area field. The result will be included in the Image format list.
Enter the number of lines and columns to be clipped, in the Top, Bottom, Left
and Right fields.
Click the Interactive button if you want to define clipping borders directly in
the image. This button is only available if the active image buffer contains an
image at the full resolution (1 x 1 binning) of the logical input channel. A red
frame will appear within the image. This frame can be enlarged or made
smaller by keeping the left mouse button depressed and adjusting the frame
size by moving the mouse accordingly. Position the frame by moving the
mouse (the left button no longer depressed). Rightclick to confirm the frame.
The part of the image outside the frame will be cut off.
Click the No Clipping button to reset all values back to zero ("0") - meaning
that no borders will be clipped. The Image format field once more displays
the largest possible image format.

35
For estimation purposes, the Active area field will provide you with a sche-
matic preview of how much area is to be clipped at the image borders. The
blue frame represents the maximum image format available for this logical
input channel. The crosshatched area represents the image area. The white
areas represent the borders to be clipped.
Note Due to Morada's large image area, you may have a larger field of view than
the field of view of the specific TEM. These undesirable shading effects
modify the image histogram so that some functions, such as the autoexpo-
sure functions, no longer work properly. You should thus set the clipping
values so that the shading effects are cut off during acquisition.
Morada • Configuring the input channel

Set the clipping values in


such a way, that the shading
effects are cut off. The
crosshatched area repre-
sents the image area. The
white areas represent the
borders to be clipped.
36
Quick-start Installation

Quick-start Installation
This section serves as a guide for those who have installed a Morada
system before. It is a quick reminder for a sequence of steps that should be
followed for a successful installation.
If you are installing for the first time, please skip this section and read all
other sections carefully before beginning the actual installation.
The basic installation steps are:
1) Install a FireWire board if not yet existing.
2) Flood the TEM column with air.
3) Remove TEM flange cover.
4) Remove protective cover on prism.
5) Install Morada unit.
6) Connect pneumatic hose with T-joint to pressurized air supply.
7) Connect pneumatic hose from Morada controller unit (connector Air In)
to self-closing valve.
8) Connect the pneumatic hoses from Morada controller (connectors A
and B) to Morada camera unit (the hose from A belongs to the
connector closer to the prism).
9) Connect "Morada In/Out" handbox to the "Morada controller"
(connector Handbox).
10) Connect the cable from the Morada controller (connector PC) to the
serial port on PC (normally COM2).
11) If your >TEM can be controlled by the image analysis program, connect
the cable from the TEM's remote control with one of your PC's serial
ports (usually COM1).
12) If your TEM can be controlled by the image analysis program, install the
software for the remote control. Please note that for some micro-
scopes, when your image analysis program is installed, the remote
control is also installed with it.
13) Connect the DB25 cable to the Morada camera cooling.
14) Install the image analysis program.
15) Install camera driver.

37
16) Connect the cable from the Morada camera unit to the FireWire board
your PC
17) Setup the remote control for all input channels, if this option is avail-
able.
18) Focus the camera.
19) Acquire offset and gain correction images for the two image formats.
20) Calibrate input channels.

Related Topics
FireWire board IEEE-1394 . 41
The Morada system . 42
Software-Installation . 53
Controlling the Morada via software . 4
Focusing the camera . 70
Morada • Handling and Usage Precautions

Handling and Usage Precautions


Important Please read the following carefully, before you attempt to install the camera.

The Morada Camera Unit


Warning! • Install your image analysis program first, before connecting the
camera to the FireWire board.
General Warning! • The Morada is shipped fully assembled, tested and ready for mounting
on your microscope. Do not adjust any part of this assembly unless it
is absolutely necessary.
• The quality of the image should be evaluated to decide whether it is
necessary to focus the Morada lens system. You will find instructions
on how to do this in the section "Focusing the camera" auf Seite 70.
38

A Morada, shown without its casing.

• The prism is shipped with a protective cover. The fluorescent coating


on the top surface of the prism is very delicate and is easily damaged.
Don't remove this cover until immediately before you mount the unit on
your microscope. Do not touch the fluorescent coating. If it needs
cleaning, gently blow clean, dry air over it.
• Remove the transportation lock.
The Morada Camera Unit

Removing the transporta-


tion lock.
The position of the transpor-
tation lock screw is indicated
by a circle.

Prism with cover still on.


Unscrew the two small
screws, then remove the
cover just prior to mounting

39
the prism unit on your micro-
scope.

• Before you install the unit, make sure that the camera-prism mecha-
nism is in the OUT position.
Morada • Handling and Usage Precautions

• Do not open the regulating valves (which control the pre-adjusted cam-
era unit's speed of movement) too far.
• Exposure to high temperature or humidity will affect the system's char-
acteristics. Avoid storage or usage in such conditions.
• Do not subject the camera to mechanical shock.
• The FireWire cable plug is not symmetrical. You must therefore make
sure that the cable plug is facing the same way as the camera socket,
when you plug the cable into the camera connector and the FireWire
PCI board.
• Do not disconnect the FireWire cable while your image analysis pro-
gram is running.
• Wear protective gloves when you handle the camera.

The FireWire board IEEE-1394


Warning! • The Fire Wire board's components can be very easily damaged by stat-
ic discharge. Wear grounding wrist straps when handling them.
• Do not plug any cards into the PCI slot, or unplug any out of it, while
your PC is switched on.
• Please follow the cable installation procedure in this manual step by
step to avoid making any incorrect connections. Incorrect connections
may result in serious damage to your PC system and/or the camera.

The Morada Controller


• If, for any reason, you need to disconnect the pressurized air supply,
make sure that the prism mechanism is in the Out position. You may
encounter some problems in moving the prism mechanism later, if
pressurized air is reconnected when it is in the In position.
• The air pressure requirement is 4 - 6 bar. Air pressure outside this
range may cause the unit to operate incorrectly or cause mechanical
damage to the camera mechanism.
40
Camera Installation Procedure

Camera Installation Procedure


FireWire board IEEE-1394
When is this necessary? The installation of the Fire Wire board is only necessary if your PC does not
have a built-in FireWire interface or and s not yet equipped with a FireWire
board.
Illustration. 1: The FireWire
board that is delivered
together with the Morada.

Installing the FireWire board


1) Turn off the PC and disconnect the power supply.
2) Remove your PC's housing.
3) One PCI slot is required for the FireWire board. Plug the board into the
slot (see Illustration 2).
Illustration. 2: The Fire Wire
board in the PCI slot.

41

4) Replace you PC's housing.


Morada • Camera Installation Procedure

The Morada system


How to install the Morada
1) Remove the housing. There are four small screws located on the top of
the housing.
2) Remove the protective cover.
Illustration. 3: On the top of
the housing there are four
screws. There is an addi-
tional screw at the bottom of
one side of the housing.
To be able to take off the
housing, you will have to
remove all five screws.

Illustration 4: Here, the


housing has already been
removed.
42

3) Make sure that the prism is seated firmly on the supporting bars.
Note The camera is delivered with the prism position pre-adjusted to go with your
type of microscope. So usually, you don’t have to change the prism position.
Should it, however, be necessary to do so, please abide by the instructions
that follow.
4) Make sure that the supporting bars that hold the prism are firmly
seated.
5) Flood the microscope's camera chamber with air, then remove the
camera port cover flange.
6) Make sure that the O-ring and flange surface are clean.

Related Topics
Focusing the camera . 70
Adjusting the prism position . 70
The Morada system

7) Remove the two small screws holding the prism cover, then remove
this protective cover. Check that there are no dust particles on the fluo-
rescent coating.
Note Please take especial care that the fluorescence screen does not get
damaged when you remove this cover.

Illustration. 5: Remove the


two small screws holding
the prism cover in place.

8) Place the Morada unit onto the camera port and tighten the screws.
The Morada unit is rather heavy and may require one person to hold it
in place while another tightens the screws. You may well need to use
a straight (or hex ball) Allen screwdriver or key, to tighten these screws.
Regular L shaped Allen-key drivers may not be practical due to space
constraints around the flange screws. This situation may vary from
TEM model to TEM model.

43

Related Topics
General Warning! . 38
Morada • Camera Installation Procedure

Illustration. 6: This is how


you mount the Morada unit
on your TEM.

Illustration. 7: Tighten the


Morada's retaining screws
on your microscope. Note
that the flange and position
of the screws may differ
from microscope to micro-
scope.
44

9) Put the housing back on the Morada unit.

Related Topics
Focusing the camera . 70
The Morada system

Illustration. 8: The Morada


unit mounted on the micro-
scope.

45
Morada • Camera Installation Procedure

Serial plug for COM1 Serial plug for port


port on TEM

Morada camera
Remote control se-
rial cable
Plug to
Fire Wire

FireWire cable
TEM column

Serial plug for


COM2 port
DB25-DB25 cable

PC with Fire Wire port and analy-


DB9-DB9 cable

SIS software.
DB9 cable

Morada control box


46

Air In
Out A Out B

Connection
for the camera
Serial port to
the Handbox
Serial plug for COM2
port
Pressurized air supply

Illustration. 9: The illustration shows the connections for a typical setup. The water cooling system is not shown in this
illustration. Microscopes may have the camera port at different locations.
Morada controller unit

Morada controller unit


Hoses and valves The Morada controller is shipped with three hoses and two separate valves.
1) 1 length of tubing with a T-joint on one end and a quick-connector (F)
on the other end (see illustration 10).
2) 1 length of tubing with a quick-connector (M) on one end.
3) 1 plain length of tubing.
4) 2 regulating valves.
Illustration. 10: Length of
tubing with a T-joint and a
quick-connector (F). Note Self-closing valve
Quick-connector
that the size and type of
pneumatic fittings may
differ, depending on the
model of the microscope.
For this reason the parts
that you receive may well
look different to the ones
shown here. Their functions,
however, remain the same.

T-join
T-joint

Illustration. 11: The hose


with the quick-connector
is to be joined to the Morada
controller's Air in input. Self-closing valve(F)
Quick-connector

47

Connecting the hoses and cables to the control unit.


1) Prepare the pressurized air system and a pneumatic hose for an air
pressure of 4 - 6 bar. Turn off the air pressure and cut this hose, then
connect the T-joint between the two ends. This hose may also be
connected directly to a free pressurized air outlet – in this case the T-
join will not be required. The open ends of the hoses are connected as
shown in the illustration.
Morada • Camera Installation Procedure

1. Push in
Illustration. 12: Connecting
an open ended pneumatic
hose to an air inlet/outlet.
2. Screw up tightly

2) The second hose with the quick connector (M) is to be connected to the
Air In connection at the back of the Morada controller (see illustration
13 (8)).
Note Every connection with a screw joint should be screwed up tightly. When you
do this, though, don't use excessive force.

Illustration. 13: The back


panel of the Morada control
box. (1): Connection to the 1
camera, (2): Trigger input 2
and Trigger output,
(4): serial port to the PC on
which your image analysis
program is installed, 6
(5): serial connection for the
4 5 7 8 9
handbox, (6): power supply
for the camera controller,
(7): pressurized air input,
(8): pressurized air supply
from the compressor, 3) The two connections with regulating valves are to be connected to the
(9): pressurized air outlet. pressurized air connections on the Morada housing. To do so, plug the
free ends of these hoses firmly into the air connections.
4) The Morada housing is connected to the control box by the hoses
without any other components. The hose connected to outlet 7 on the
controller unit (A) side has to be connected to the inlet which is closer
to the prism on the camera side.

Connecting the handbox to the control cable.


1) Connect the "Morada In/Out position" control box (handbox) to the
48

serial port marked Handbox on the Morada control box (see illustration
9).
" You can use this control box to manually move the prism between
the IN and OUT positions.
Installing the water cooling

Illustration. 14: The "Morada


In/Out position" control box
(handbox). This box must be
connected to the serial port
marked Handbox on the
Morada control box.

2) Use the supplied DB9-DB9 serial cable to connect the Morada control
box with a free serial port on your PC (normally COM2) (see illustration
9). Tighten the connectors with a small screwdriver.
3) Most microscopes have a remote control feature. For this you will need
an additional serial connection (usually COM1) between the micro-
scope and the PC that runs your image analysis program, which is not
in your camera's scope of supply.

Installing the water cooling


This section only provides you with an overview of how the water cooling is
installed. It's intended for people who have already gained experience with
the installation process. Should you not have had any such experience,
please make use of the separate booklet that is also supplied.
General remarks Please note that when you install the water cooling you will often find that
your microscope's cooling system has been modified over a period of time,

49
and is therefore no longer in the condition in which it was originally shipped.
For this reason the specifications in the cool system's documentation may
not be applicable anymore.
The camera, and the hoses connected to it, only require a very small amount
of water (< 0.25l), that can be handled even by inefficient cooling units. The
same applies to the cooling capacity. We recommend you to set the flow rate
at about 2 l/h to 5 l/h.

Installation on existing cooling water connections.


Proceed according to these instructions when the TEM's cooling system has
both an input and an output connection free.
When you are trying to determine how long the hoses will have to be, it is an
advantage if you have already mounted the camera on your TEM.
Before you begin the installation, make sure that you have all of the compo-
nents you need, on hand. The following parts will be delivered with your
shipment:
Morada • Camera Installation Procedure

• 2 lengths of water tubing (6 mm)


• 2 quick-release connectors (M)
• 1 rotameter
• 1 stand for rotameter
• 2 CPC connectors (M)
1) Shut down your microscope according to the manufacturer's instruc-
tions.
2) Wait for half an hour, then turn off the cooling.
" In this way you will have made sure that the device's lenses have
cooled down sufficiently.
3) Connect the CPC connectors to the 6mm water hoses.
4) Push the hoses onto the camera's water connections.
5) Determine where you want to have the rotameter, and cut the hose
leading from the water intake to the camera's upper water connection,
to the required length.
6) Push the free end of this hose that comes from the camera, into the
rotameter's upper connection.
7) Push the other free end into the rotameter's lower connection.
8) Close the rotameter's valve tightly.
9) Connect the warm water return hose coming from the camera to one of
the cooling system's free inlets.
10) Connect the cold water supply hose to one of the cooling system's free
outlets.
11) Start the cooling system.
12) Use the DB25 cable to connect the Morada camera unit to the camera
controller.
Note Take care that the DB25 cable is correctly orientated! One end of the cable
fits onto the camera housing, the other end onto the controller. Connect the
DB25 port to the camera controller. Plug the other end of the cable (i.e. the
flat port) into the socket on the camera unit.

Installation where no cooling water connection is available


50

Follow these instructions when the TEM's cooling system has no free
cooling water connections for the camera. In this case the cooling circuit has
to be interrupted, and two branches inserted. These branches must be
equipped with self-closing connectors, so that the camera can be removed
without any further work.
Installing the water cooling

Illustration. 15: Schematic


diagram of the cooling water Camera housing
circuit

rota-
meter

from TEM

to TEM

Before you begin the installation, make sure that you have all of the compo-
nents you need, on hand. For this, the dimensions of the hoses have to be
known.
Decide on a suitable place for making a branch in the cooling water system.
It must be accessible for installation work.
• 2 hose clamps
• 4 hose nozzles with 8 mm diameter
• 2 prepared T joints with quick connections (F)
51
1) Carry out the steps 1 to 8 from the "Installation on existing cooling
water connection" (siehe Seite 49) instructions.
2) Check whether the TEM's cooling system uses 1/2" hoses or 8mm
hoses.
" The T-joints are equipped with nozzles for 1/2" hoses.
" Should the system use 8mm hoses, unscrew the nozzles from the
T-joints and replace them with the separate nozzles for 8 mm diam-
eter hoses.
3) Attach both of the hose clamps to the cooling system's input hose.
" The two hose clamps should be about 20cm from each other.
4) Mark the cutting spots with two stripes.
" The distance between the cutting points should be equivalent to the
T-joint's length.
5) Cut through the hose at the points you've marked.
6) Lay the ends of the hose with the clamps on, in a basin filled with water.
Morada • Camera Installation Procedure

7) Lay the T-joint in the water also.


" The T-joint should then fill with water.
8) Push the ends of the hose onto the T-joint.
" Make sure that when you do this, all of the elements remain under
water.
9) Release the clamps, then repeat the steps 3 to 8 with the cooling
system's outlet hose.
10) Push both of the quick-connections (M) onto the free ends of the hoses
that lead to the camera.
11) Push the quick connections onto the corresponding connectors on the
T-joints.
" The T-joint in the supply line must be connected to the rotameter.
12) Use the DB25 cable to connect the camera unit to the camera
controller.
Note Take care that the DB25 cable is correctly orientated! One end of the cable
fits onto the camera housing, the other end onto the controller. Connect the
DB25 port to the camera controller. Plug the other end of the cable (i.e. the
flat port) into the socket on the camera unit.
" You can now install your image analysis software.
Important Do not plug in the FireWire cable yet! You have to connect the FireWire
cable after installing the image analysis software, to allow the program to
find the correct driver.
52
Software-Installation

Software-Installation
Remote control software
Remote Control driver Remote control is available for some later models of microscopes. It allows
software your image analysis program to read some microscope parameters, such as
magnification, via the serial port. It is also used to send control commands
to the microscope, such as moving the sample stage.
Certain models of microscope require a separate installation of the Remote
Control driver software. This should be done before installation of your
image analysis program. This software is normally supplied in a separate
disk media and installation instruction.
For some models of microscope the remote drivers will be installed during
installation of your image analysis program.

Image analysis program, camera driver, and remote control


System requirements The Morada camera requires the FIVE analySIS iTEM and Microsoft
Windows XP (or higher). Your image analysis program also supports multi-
threading on multiprocessors, thus making full use of the power of the latest
multi-CPU PC’s.
Camera driver installa- Installation of the Morada camera driver starts via your image analysis
tion program setup. You are required to specify the camera driver during setup.
Then you have to get Windows to use the Morada camera driver.
Installation of iTEM Installing the image analysis program iTEM is a simple process, you simply
follow the onscreen instructions.
1) Place your image analysis program's installation CD in the CD-ROM
drive.
" The setup program will start automatically - unless you have deac-
tivated the autorun function. If you have, start the setup.exe file
manually via Windows Explorer.
" The analySIS FIVE Setup dialog box will be opened.

53

Related Topics
Camera driver installation . 63
Morada • Software-Installation

The analySIS FIVE Setup


dialog box

2) Click the analySIS FIVE line, to start the installation of your image anal-
ysis program and the camera-driver.
" The License agreement dialog box will be opened.
Read all of the license
agreement carefully.
54

3) Click the Yes button to accept the license agreement..


" The iTEM language dialog box will be opened.
" If you don't accept the license agreement the set up will be
canceled.
Image analysis program, camera driver, and remote control

The iTEM-Language Selec-


tion dialog box.
Which languages will be
offered you there, depends
on which operating system
you are using.

4) Select the language in which your image analysis program's user inter-
face is to be displayed, and click the Next> button.
" The Customer Information dialog box will be opened.
The Customer Information
dialog box.

55

5) Enter your name, and the name of your company, in the respective
fields, then click the Next button.
" The Registration Confirmation dialog box will be opened.
Morada • Software-Installation

The
Registration Confirmation
dialog box.

6) Check the details in the Registration Confirmation dialog box, then click
the OK button to confirm them.
" The Microscope Selection dialog box will be opened.
The Microscope Selection
dialog box.
56

7) Select the manufacturer of your microscope in the Manufacturer list,


and the model in the Microscope list. Then click the Next > button.
" The Image Source Selection dialog box will be opened.
" In these lists, all of the microscopes that your image analysis
program can control by remote control have been included. Should
your microscope not be included, this will mean that no remote
control is available for it. In this case don't select any microscope.
Image analysis program, camera driver, and remote control

The Image Source Selec-


tion dialog box.

8) In the Image source list, select Cameras > Olympus Soft Imaging Solu-
tions and in the Device list the Morada check box.
" Your image analysis program can operate several different
cameras simultaneously. In this case, you should select all of the
cameras you have connected up.
" The Install Demo-Database dialog box will be opened.
The Install Demo-Database
dialog box.
You will be offered two
different databases.

57

9) Select the database you want, then click the Next button.
Morada • Software-Installation

" The "Example Database" database contains general examples for


image processing, the "iTEM" database, special examples that
have been acquired with electron microscopes.
" The Install NetCam dialog box will be opened.
The Install NetCam dialog
box.
With NetCam, your
camera's live-image can be
transferred to other
computers.

10) If you want to use the NetCam add-in, select the Yes, install option. In
this case, you will also have to install a web server, should one not yet
be available on your PC. Then click the Next > button.
" The Choose Destination Location dialog box will be opened.
" When the installation has been completed, you will find further infor-
mation on NetCam and the necessary web server, in your image
analysis program's "Module\NetCam subfolder, in the
"NetCam_Info.pdf" file.
58
Image analysis program, camera driver, and remote control

The Choose Destination


Location dialog box.
A destination folder will be
automatically suggested by
the setup.

11) Check if the destination folder that has been suggested is the right one,
then click the Next> button. Should you want to select, or create,
another folder for the installation, first click the Browse... button.
" The Confirm New Folder dialog box will be opened.

59

12) Click the Yes button.


" An additional Choose Destination Location dialog box will be
opened. In this dialog box you determine in which folder the
example databases that you selected in step 9, are to be installed.
Then click the Next > button.
Morada • Software-Installation

The Choose Destination


Location dialog box for the
installation of the example
databases.

" The Select Program Folder dialog box will be opened.


The Select Program Folder
dialog box.
60

13) Enter the name you want for the program folder, in the Program Folder
field, then click the Next > button.
" The installation will then begin. Its progress will be shown in the
Setup Status dialog box.
Image analysis program, camera driver, and remote control

The Setup Status dialog box


gives you information on the
installation's progress.

" When the installation has been completed, you can immediately
start your image analysis program.

61
Morada • Software-Installation

Camera cable
How to connect camera and PC
1) Plug the shielded end of the FireWire cable into the camera socket.
" The FireWire cable plug is not symmetrical. You must therefore
make sure that the cable plug is facing the same way as the camera
socket, when you plug the cable into the camera connector. Other-
wise the camera can be damaged.
Make sure the cable plug is
facing the right way before
you plug it into the camera
socket.

2) Plug the other end into one of the free connector sockets on your PC's
FireWire PCI board.
" There are two or more connector sockets, depending on the type of
FireWire board that has been inserted. You can use any of them.
3) Continue with the camera driver installation before you start your image
analysis program.
62
Camera driver installation

Camera driver installation


After you have installed your image analysis program and connected the
camera to the PC - or vice versa - the Found New Hardware Wizard dialog
box will automatically be opened.

You have to go through the following steps to get Windows XP to use the
correct camera drivers.
1) Select the No, not this time option and click the Next > button.

63
Morada • Software-Installation

2) Select the Install from a list or specific location (Advanced) option, then
click the Next > button.

3) Select the Don’t search. I will choose the driver to install. option, then
click the Next > button.
The Soft Imaging System -
Morada(20) driver has been
found.
64

4) Select Soft Imaging System - Morada(20) from the list.


5) Click the Next > button.
" The following dialog box will appear.
Camera driver installation

6) Click the Continue Anyway button.


" The Hardware Update Wizard dialog box which had been in the
background, will become visible.
" When you have finished the Morada camera driver installation the
following dialog box will be opened.

65

7) Click the Finish button.


" The Hardware Update Wizard dialog box will be closed.
" The camera is now ready for use.
Morada • Troubleshooting

Troubleshooting
What to do when the 1) Open the Windows Device Manager via Start > My Computer > (right
siscamfw driver has not mouse) > Properties > Hardware > Device Manager... .
been found.

" The Device Manager dialog box shows the Generic 1394 Desktop-
camera entry in the Imaging devices section.
2) Select the siscamfw entry and click the Update button in the device
manager button bar.
66
Troubleshooting

3) Select the Install from a list or specific location (Advanced) option and
click the Next > button.

4) Select the Don’t search. I will choose the driver to install. option and
click the Next > button.

67

" The Model list contains the siscamfw entry.


5) Click the Next > button.
Morada • Troubleshooting

" The next Hardware Update Wizard dialog box will be opened in the
background, displaying the message to wait while the Wizard
installs the software.
" Additionally, the Hardware Installation dialog box will pop up in the
foreground.

6) Click the Continue Anyway button.


" The Hardware Update Wizard dialog box which had been in the
background, will become visible.
" When the Morada camera driver installation has been completed,
the following dialog box will be opened.
68
Service Notes

Service Notes
Warning The instructions in this sections are for service technicians only. If you
encounter any problems while installing the camera, please contact our
support desk.
Warning! • Always remember to move the Morada to the OUT position (out of
beam path) before removing the pressurized air supply from the
Morada control box. The green button on the In/Out position control
box should be lit. If the Morada was left in the IN position, you may have
an air leakage when you reconnect the air supply.
• The inlet valves on the Morada unit are pre-adjusted for normal in/out
movement speed. Opening the valves too far may cause the unit to
move too fast, thus causing mechanical damage. If adjustments are re-
quired, make them in small increments and always start from the
closed position.

Adjusting the Morada In/Out movement speed


How to adjust the Morada In/Out movement speed
Warning! The Morada does not need to be taken from its mounting during the instal-
lation, except when the lens system needs to be focussed. Therefore these
notes are only relevant when there is a need to service the unit.
1) The valve with which the speed the prism moves is regulated, is located
on the hose for the pressurized air supply, nearest to the camera.
2) Closing a valve will cause movement to slow down and opening a valve
will increase the speed. If the valve is closed too much, it may not move
at all. If the valve is opened too far, it may move too fast. You should
adjust the valves in such a way that the movement between the two
positions takes approximately 2 seconds.
Position of the valves that
control the speed of the IN
or OUT movement.

69
Morada • Adjusting the prism position

Adjusting the prism position


Warning You are normally not required to disassemble any part of the Morada system
during the installation, except for the purpose of focusing the lens system.
Therefore these notes are only necessary if there is a need to service the
unit.
Note The prism position varies with the model of microscope. The camera is deliv-
ered with the prism position pre-adjusted to your type of microscope. So
usually, you don’t have to change the prism position.
When is this necessary? You only have to adjust the prism position when the shadow of the prism on
the microscope fluorescence screen is not symmetric.
This is what the shadow of
the prism should like on your
microscope's fluorescence
screen.

How to adjust the prism position


1) The prism can be moved by several millimeters. This adjustment is
typically done to center the prism in the microscope's field of view.
2) On the underside of the prism there are two screws that fasten it to the
two supporting bars, the so-called prism support. Loosen these
screws and slide the prism to the required position, then tighten them
again. Keep the face of the prism parallel to the face of the flange.
3) Follow the procedure in the next section to refocus the camera's lens.

Focusing the camera


Warning! You are normally not required to disassemble any part of the Morada system
70

during the installation, except for the purpose of focusing the lens system.
Therefore these notes are only necessary if there is a need to service the
unit.

How to focus the camera


1) The camera should be focused while the system is running. On some
models of microscope a beam stop, located above the scintillator, is
available, with it you can easily focus the camera. Otherwise you will
have to focus it with the scintillator surface.
2) Check the distance from the front of the flange surface to the middle of
the prism. This distance varies with the model of the microscope.
3) Check that the prism supporting bars are firmly seated.
Focusing the camera

4) Use an input channel with the following settings:


" 2004 x 1336 image size format with 2x2 binning,
" Exposure time - 50 ms,
" Histogram display - off,
" Automatic gain display - on,
" Real time FFT - on,
" Shading correction - off.
Warning! Never loosen the prism supporting bars at this point, since the vacuum could
suck the prism, together with the supporting bars, into the column, with
disastrous consequences.
5) Loosen the camera's securing screws.
The positions of the 5
securing screws are marked
in the illustration.

6) Bring your specimen into focus by using the microscope fluorescent


viewing screen.
7) Use the micrometer screw to move the Morada unit into the beam path.
The micrometer screw.

71

" You can achieve a more precise focus by using the RTFFT spec-
trum. An optimally focused image has the maximum spectral
spread (more high frequency information), i.e., the greater the
distance of an image structure from the center, the better.

Related Topics
Switching the shading correction on and off . 12
Morada • Focusing the camera

The fourier image of a 2-D


catalase crystal.
The light spots represent the
periodic structures in the
microscope image. When
the camera is better focused
the spots move further away
from the center of the
image.

8) When you are satisfied with the focus, tighten the camera securing
nuts.

Focusing the camera by using structures on the fluorescence


screen
How to focus the camera by using structures on the fluores-
cence screen
1) Start the live mode.
• You can make use of the Morada's Intelligent Exposure function to do
this.
2) Activate the RTFFT function.
" In the RTFFT display the structures make a circular spot around the
central beam.
72

Related Topics
Activating RTFFT . 21
Acquiring images with Intelligent Exposure . 14
Focusing the camera by using structures on the fluorescence screen

The RTFTT Display dialog


box when the camera is out
of control. The spot is quite
small.

3) Remove the specimen from the light path.


4) It is easier to focus the camera when the contrast is enhanced and the
brightness is kept reasonably low.
Move the Contrast slide control on the Visualization tab of the RTFFT
Control dialog box to the right in order to increase the contrast.
Move the Brightness slide control to the left in order to decrease the
brightness.
5) Use the micrometer screw to move the prism in such a way that the
spot increases in size.
Move the prism along the
rod with the micrometer
screw designed for this
purpose, until the cluster
occupies most of the RTFFT

73
Display window.
Morada • Appendix

Appendix
Technical specifications
Image resolution Standard resolution: 4008 x 2672
2x binning: 2004 x 1336 pixel
4x binning: 1002 x 668 pixel
8x binning: 500 x 334 pixel
Pixel size 9 x 9 µm (both on chip and on scintillator)
Pixel clock rate Single snapshot (Snapshot mode): 12 MHz
Live acquisition (Acquire mode): 24 MHz
Dynamic range 16384 gray levels @ 14 bit
Exposure time 100 µs - 160 ms
Frame rate (depending on reso- Standard resolution: approx. 2 fps
lution and PC speed) 2x binning: approx. 3.8 fps
4x binning: approx. 6.6 fps
8x binning: approx. 10.3 fps
Partial Readout: approx. 8.2fps
Display Full image at any frame rate
Cooling element 15°C, Peltier cooled
Temperature monitor CCD chip & Housing
Camera mount One flange at wide angle port
Camera positioning PC controlled pneumatic movement / control
box
Optical Coupling Lens-optically coupled
Anti-Blooming > 60000 e-
Interface FireWire (IEEE1394)

Packing List
1) Morada camera unit assembly.
2) Flange screws.
3) Morada control box.
4) Morada In/Out position control box (handbox).
74

5) analySIS PC with software and installed FireWire board (when a


complete system is shipped).
6) Special FireWire cable (PC to camera).
7) DB25-DB25 serial cable (PC to Morada control box).
8) DB9 cable (Morada In/Out position control box to Morada control box).
9) DB9-DB9 serial cable.
10) 2x bare pneumatic hoses (5mm ‡). (Morada control box to Morada
camera unit).
11) 1x pneumatic hose (6mm ‡) with connector to self-closing valve on
one end.
12) 1x pneumatic hose (6mm ‡) with self-closing valve on one end and T-
joint on the other end. The size and type of T-joint may vary for the type
of microscope of pneumatic system in use.
13) Image analysis software package.
14) This User’s guide
CE declaration

CE declaration

75
Morada • WEEE DECLARATION

WEEE DECLARATION
Declaration of Confor- In accordance with European Directive 2002/96/EC on Waste Electrical and
mity Electronic Equipment this product manufactured by Olympus Soft Imaging
Solutions GmbH must not be disposed of as unsorted municipal waste, but
should be collected separately. The end user should refer to his local distrib-
utor for return.
76
Index

Image Rotation 30
A Input 4
Acquire Images 4 Calibrate 17
Adjust Configuring the input 28
In/Out movement speed 69 Duplicating already existing input 28
Prism position 70 Intelligent Exposure 14
Automatic Gain Display Exposure time correction 15
Camera Control 24 intX
Resolution 16

C
L
Camera Control 5, 24
Automatic Gain Display 24 Live Acquisition
Exposure time 24 Intelligent Exposure 15
Partial Readout 27 Live overlay 33
Sharpness Monitor 26
Camera resolution
in intX 16 M
Check reference images 13 Morada System 42
Configure Input
Input 29
O
E Offset image 8
Online shading correction 7
Exposure time
Camera Control 24
P
F Partial Readout 27
Prism supporting bars 42
FireWire board IEEE-1394 40

77
Installation 41
Q
Fixed scaling 25
Focus camera 70
Quick-start installation 37

G
Gain image 7
R
Remote control 22
Resolution
H intX 16
Rotation 30
Handbox 48 RTFFT Control 21

I S
Image acquisition Service Notes 69
RTFFT Control 21
Index

Set Magnification 22
Sharpness Monitor 26
Snapshot 6
Intelligent Exposure 15
Software Installation 53

T
Trigger Mode 30
78