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Analyze videos of moving color circles (cells) to extract rules/patterns?

Posted 6 years ago

I have videos of cells moving around a dish (2D). The cells are in different colors, representing various physiological states, and the colors change with time. What I need is some sort of unbiased machine learning approach, to look for patterns and relationships between color and movement. For example, do cells of a specific color tend to touch each other more than different colors, or do specific kinds of contact lead to a color change shortly thereafter? Basically, to extract any possible relationships between movement, relative position, and color. What is an appropriate technique for that, and are there any existing packages that do this (or people interested in writing us some analysis code as a contractor project)?

POSTED BY: Michael Levin
5 Replies

Did you make any progress? I work on movement analysis of animals, including social groups, and I don't see why it would be any different looking at interacting cells. I think there are two separate parts to your problem: the cell tracking and the movement analysis. Depending on your video the tracking might actually be easy, and there are lots of established methods. As for the analysis, one part of your question (about touching) sounds like you want to build association matrices and look for patterns in those. What I work on is modeling movement trajectories in relation to other objects in the vicinity (including other individuals/cells). This is not standard, although there are a few different techniques.

POSTED BY: Gareth Russell
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Posted 6 years ago
POSTED BY: Anonymous User
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Posted 6 years ago

From what I understand, you may have to learn matrix algebra to understand Convolve (unless Mathematica examples found by google suffice what you need). You'll have to do some programming to get colors, position, motion. And even if that pops out of an advanced matrix: you have to code an interpretation. It would give you position, color, motion and is possible: I didn't say easy, I haven't seen your "video". Previous posts have asked about cell outlining before (you can search for those posts they HAVE EXAMPLES already made).

If you decide to do machine learning you don't get out of coding. You have to code it to recognize what your looking for in it's distinct language! (plus you have to code the niches needs of the ml itself).

(your other option, unless your crafty or find nueralnet code that does it or are a matrix wizard: is to write math script to check values exactly as you need: overlap (hit) per color, frequency stats, and show running stats perhaps)

It becomes a coding preference and if your serious about getting meaningful repeatable results: my guess is unless you google and find code for it, it will be allot of coding to do.

POSTED BY: Anonymous User
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Posted 6 years ago
POSTED BY: Anonymous User

I am no expert on this, but there are built-in functions that may help: ImageFeatureTrack, MorphologicalComponents.

POSTED BY: Gianluca Gorni
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