ListofFreeSoftwareforMicroscopy

CompiledbyRainerHeintzmann(KingsCollege)fortheAQLMcourse,2009

Dataacquisition

Micromanager
http://www.micromanager.org/

CamAcqJ(GrantHarris)
Acquisition&Instrumentcontrol.SupportsQImagingandLuminaracamerasand
variableretardersandstages.
http://www.mbl.edu/research/labs/adlc/CamAcqJ/

ScanImage(VijayIyer,KarelSwoboda)
Developedfor2photonmicroscopyandneurobiology/patchclamping
http://research.janelia.org/wiki/display/ephus/ScanImage

DisplayandSegmentaton
BioimageXD
3DVisualisationandanalysis(nicerendering)
UniversityofTurku&UniversityofJyvskyl,Finland
Linux/Mac/Windows,VTK+Pythonbased(latestupdate:20080328)
http://www.bioimagexd.net

VisBio(CurtisRueden&AbrahamSorber),
3DVisualisationandanalysis(nicerendering).
InterfaceswithOME.(latestupdate:9Mar2009),
http://www.loci.wisc.edu/visbio/

V3D(HanchuanPeng)
Greattoolsforvisualizationandsegmentationoflarge(!)datasets.
3Dannotation,landmarking,datamanagement,cellsegmentation,neurontracing,
deformableregistration,andmore(latestupdate2009May5)
http://hanchuan.peng.googlepages.com

ImageProcessing

COSMOS=COSMOpenSouce(ChrysanthePreza)
soontocome.Havealookat:,http://cirl.memphis.edu/cosmos

ImageJ:ApublicdomainJavaimageprocessingprograminspiredbyNIHImage
fortheMacintosh.Windows,MacOS,MacOSXandLinux.
Plugins(http://rsb.info.nih.gov/ij/plugins/)supportvariousmicroscopyrelated
issues.E.g.timestamping,resampling,tracking,LOOKHEREFIRST
http://rsb.info.nih.gov/ij/


DeconvolutionLab(GuillaumeSchmit,EPFL)
ToolboxforImageJwithvariousdeconvolutionalgorithms.Someofthemarestate
oftheartwaveletbasedconstraints.Only2^nsizedimages!
AskDanielSage(daniel.sage@epfl.ch),EPFLifinterestedinusing.

3D_Deconvolution(PierreBesson,CdricVoneschandFranoisAguet,EPFL)
3DdeconvolutionpackagewithPSFgeneration.Only2^nsizedimages.
http://bigwww.epfl.ch/demo/deconvolution3D/

IterativeDeconvolve3D(BobDougherty,OptiNav,Inc.)
Memoryintensitve.
http://www.optinav.com/imagej.html

DeconvolutionJ(NickLinnenbrgger)
http://rsb.info.nih.gov/ij/plugins/fftj.html

Voxx:AVolumeRenderingProgramfor3DMicroscopy.Voxxisavoxelbased(not
surfacebased)3Drenderingprogramwhichhasbeenoptimizedforbiological
microscopy.Thissoftwarepermitsresearcherstoperformrealtimerenderingof
largemicroscopydatasetsusinginexpensivepersonalcomputers.Wedevelopedit
toexplore3Ddatasetscollectedonconfocalandmultiphotonmicroscopysystems,
butitcanalsorenderotherkindsofdata(e.g.CT,MRI,etc.).
http://www.nephrology.iupui.edu/imaging/voxx/

NIHimage(Maconly):NIHImageisapublicdomainimageprocessingand
analysisprogramfortheMacintosh.
http://rsb.info.nih.gov/nihimage/

CellProfiler(AnnCarpenter,MIT)
Versatile2Dprocessingplatformforhighthroughputscreeningapplications.
http://www.cellprofiler.org/

IrfanView+IrfanViewplugins:Batchconversion(withimageprocessing),
multipageTIFediting,TIFF,AVI,MPEG,DICOM,(lookunderviewMultipage
images,Extractimagesfromamovie,
http://www.irfanview.com/

VisBio:VisBioisabiological(3D)visualizationtooldesignedforeasy
visualizationandanalysisofmultidimensionalimagedata.
http://www.loci.wisc.edu/visbio/

IVE&Priism(Sedatlab,UCSF)
http://www.msg.ucsf.edu/IVE/index.html

Tracking

CellTracker(HailinShen,Univ.ofManchester)
Advancedandusefultoolfor2Dtrackingofcellsandfeatures.UsesSnakes.Based
onMatlab.(lastupdate8June,2006)
http://dbkgroup.org/celltracker/

utrack(Jaquaman,Danuser)
ForexpertspowerfullinkingalgorithminMatlab,
3Dispossible.ManyMatlabtoolboxesareneeded.
http://lccb.scripps.edu/content/download.html

TrackingandBallonSegmentation,2D(L.Dupuy)
Theyalsocandotrackingbutdonotshowitonthewebsite.Worthasking.
Segmentationplugingcanbedownloaded:
http://www.archiroot.org.uk

3DTracking
Websitewasdown.Butshouldbegood.Windowsonly.Zebrafishembryogenesis?
http://www.cbiplatform.net/

View5D:JavaApplet,ImageJplugin,Matlabplugin
TheprogramView5Dinteractivelydisplaysofupto5dimensionalvolumetric
datasets.
Threeorthogonalslicingviews,2Dand3Dhistogramsofintensity(scattergrams),
Basicimageprocessingoperations(ratioing,..),Interactivecountingandtaggingof
entities,Trackingof3Dmovements,Multiplicativedisplayoflifetimeorratio
images.
http://www.nanoimaging.de/View5D/

VTK:Forprogrammersonly.TheVisualizationToolKit(VTK)isanopensource,
freelyavailablesoftwaresystemfor3Dcomputergraphics,imageprocessing,
andvisualization.Moreforexpertusers,whoknowhowtoprogram.Very
powerfulandbigcommunity!
http://www.vtk.org/

BIRN:Selectionofvarioususefultoolsforimageprocessingandanalysis.Mouse
BrainAtlas,3DSlicer,LONIPipeline,FunctionalMRI,
http://www.nbirn.net/Resources/Downloads/

OME:OpenMicroscopyEnvironment
Datamanagementforbiologicallightmicroscopy.Imagebasedanalysisofcellular
dynamics.Imagebasedscreensofcellularlocalizationorphenotypes.
OMEisadatabaseenginewhichallowsalabtostoreallmicroscopyimagesalong
withmetadata;keepingtrackofprojects.Someimageprocessingfeaturesavailable.
http://www.openmicroscopy.org/

DIPimage/DIPlib:(Matlabisneededasaplatform)
ThisMatlabtoolboxcontainsalargeamountofveryuseful(oftenNdimensional)
imageprocessingalgorithms.DIPimagefeaturesitsowndatatype(dip_image)and
aconvenientbrowsertoquicklyinvestigatetheresults.
MicroscopyorientedFeaturesare:AutomaticThresholdingalgorithms,Cross
correlationbasedshiftdetermination,Segmentationalgorithms(e.g.watershed
transform),Noisefiltering(e.g.anisotropicdiffusionwithlocalstructuretensors),
Convolution,Measurementsoflabeledentities(e.g.Majoraxisdirection)
http://www.ph.tn.tudelft.nl/DIPlib/

CudaMat(RainerHeintzmann)
UsingNVidiasGPUsforfastdatacrunchinginMatlab.
Idea:Makeitsimple:myImage=cuda(myImage);
Onlyasubsetsupportedatthemoment.Datatypes:singleandscomplex
Contactme(heintzmann@gmail.com)

minFunc(MarkSchmidt)
Matlabfunctionforgeneralminimization.Lotsofmethodsimplemented.
http://www.cs.ubc.ca/~schmidtm/Software/minFunc.html