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Measuring biological matter

sabato 24 aprile 2010 13.42

Christian Lovato

What is biological matter? It is group of atoms (matter) that has (or had) the property of being alive. We don't go in the definition of wich mean "being alive", but is a common notion, learned by examples. Some examples are

A tree

A cat

A cell

A tissue

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A human

Measure: The quantity, size, weight, distance or capacity of a substance compared to a designated standard.
Incollato da <http://en.wiktionary.org/wiki/measure>

we can say "give a number (or a set of numbers) indicating something"

Measure of an artifact

Information theory
Information theory recognizes that all data are inexact and statistical in nature. Thus the definition of measurement is: "A set of observations that reduce uncertainty where the result is expressed as a quantity."[3]. This definition is implied in what scientists actually do when they measure something and report both the mean and statistics of the measurements. In practical terms, one begins with an initial guess as to the value of a quantity, and then, using various methods and instruments, reduces the uncertainty in the value. Note that in this view, unlike the positivist representational theory, all measurements are uncertain, so instead of assigning one value, a range of values is assigned to a measurement. This also implies that there is a continuum between estimation and measurement.
Incollato da <http://en.wikipedia.org/wiki/Measurement>

A mug

With some instruments

We obtain a set of Informative (useful) measures

We can define a diameter, an height, without ambiguities.

After, we can answer some questions like: how many mugs can enter in this box?

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in the biological domain the situation is usually different.

We can measure as we do with artifacts, but we have a lot of problems, for example in defining what and how to measure. In most cases biological systems cannot "fit" into a determined number of measures. For example one of the common measures of the body is stature. Measuring height is simple. A little bit more complicated than measuring the height of a mug but we can obtain a number that gives the stature of a person. However there are some problems once we want to use this number.
For instance, there is a problem with this number's precision. We know that the stature of a person changes during life, so that the temporal validity of this number is limited. And if we want to be more precise, the height of a person decrease of about 1% during the daytime and increase during the sleep. [http://www.informaworld.com/smpp/content~db=all~content=a785169438] Another order of problems that emerges is about the definition of the measure, i.e. how to deal with hairs during the measurement: if we compress them we obtain a certain number, if we don't we have another, and if we cut them and measure on the scalp we have yet another measurement.

None of them is the "real" height, every measure has a different biological meaning, if not a clinic one.
All we have said about stature is valid for almost all the measures we can think to perform.

These problems derive, as last resort, from the fact that biological systems (and thereby shapes) are complex, and we don't have a well defined geometrical, or mathematical, model of what a "human body" is.

While we can have few ambiguities in measure and use the measures of the mug, we really have a lot of ambiguities in measuring, and in using the measures of biological systems, because of their complexity. How to approach this complexity? Or, more simply, how to get objective measurements of biological systems? Firstly, we need a model of the human body. Every measure is related to a model that express some of the relationships of the subject. While for the measures of a mug we can simply define one (the measure of "diameter" is strongly connected with the notion of the "cylinder" that forms the geometrical model of the mug) in the biological case, this model is more complex and should be explicitly defined, for every set of measures we want to obtain.
The model is usually in the mind of the operator, and must be shared with the agent that uses the measurement. Different people have usually similar (not equal) models of the same subject.

Secondly, we can manage the complexity of the "human body", and of the model that should be derived from it, by means of successive refinements. We can start from simple general models, and "deepen" them into more complex and precise models that use the information obtained from the simpler ones, in a process can be compared to the successive approximation of an optimization algorithm.

These considerations lead to a general framework in wich a such model can be constructed, and in wich the notion of successive approximation is implemented.
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the notion of successive approximation is implemented.

In this very general frame we take row data as input, preprocess them in order to achieve a good precision against acquisition errors, and process them at different stages, or levels.

At every stage we refine the explicit information about the particular examined dataset . The key is that we can use information extracted at early levels to simplify (make more efficient, faster, simpler to implement) the tasks of the deeper levels.

We can expand this framework by including new data sources. We can also decide to set up interactive measures for those blocks for which automatic measures are not readily avaiable, or the implemented algorithms fail for some specific data. Other interesting features and properties of the method can be: Substitution of algorithms when better (faster, or more robust) algorithms become avaiable, alterating only a block, with eventual minor changes in neighbours blocks Measures on request: if an automatic pipe is heavy to process as a whole, only the needed blocks can be activated (backpropagation of request) Associate to every measure some indicative label (from medical domain ) Reusability of well-behaving algorithms within the system at different levels/scales, where previous stages provide the context to deeper ones. This frame fits naturally in a multirisolution approach, i.e. different levels could use data at different resolutions.

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In general, strenght of this approach is the good coupling it can give between "medical knowledge" and the implemented model, because the measures are guided from the medical needings, and the representation can give useful medical informations at all levels of frame, from the simplest ones (that give general information) to the deeper levels, that extract more specific or contextualized informations. This feature is necessary in order to obtain immediatly useful and informative measures of the subject.

Example (our anthropometric application)


What's already done at level 1

Improvements:
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Improvements:

Better mesh preprocessing -> allows analysis of fine structures; i.e. hands, that in the original mesh has motion artifacts Advanced hole closing -> refinement in volume measurement Add algorithms for interesting points on mesh surface, in order to make segmentation more robust, or make it work in presence of topological variations due to different subject poses Planning to improve the stick fitting algorithm.

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