Movement Validation Progress Report

[Jim Hokanson]

Hi all,

  Michael and I wrote up another progress report:

https://docs.google.com/document/d/1sBgMAD-7RUjHwBgrC204LMqSC81byIaZNRm32lEGWMM

  If anyone has any questions let us know.

Jim

[Stephen Larson]

Great progress you guys!  

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[Mike Vella]

Hi guys,

The paper makes a nice read. I have one question: The the route you seem to be taking is to analyse video from the simulation, but the position of all the constituent matter is known at all times for the stimulation. Have you considered using it directly?

Mike

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[Stephen Larson]

On Thu, Dec 12, 2013 at 2:55 PM, Mike Vella <vell...@gmail.com> wrote:

The paper makes a nice read. I have one question: The the route you seem to be taking is to analyse video from the simulation, but the position of all the constituent matter is known at all times for the stimulation. Have you considered using it directly?

Mike

Hi Mike -- the code base they are working with does have raw video as the starting point, but in this case they are working with the assumption that the video has already been segmented into a 'worm skeleton' and are working on the part of the pipeline that calculates statistics from that worm skeleton.  This worm skeleton ought to be the same thing produced by our simulation, so that the same statistics that were calculated on the video data can be calculated on the simulated data.  They are not looking to re-implement the image analysis code on OpenGL videos of the worm, they are interested to get exactly the output you are referencing here as their starting point.  Makes sense?

If Sibernetic generated the same kind of worm skeleton right now, they could start to compare it to real data very soon.  The format for exposing this skeleton has been defined explicitly now by these guys and there are Python objects to work with to create them.

Thanks,

  Stephen

[Jim Hokanson]

A few additional points.

At some point we had mentioned doing video extraction for the simulation although I don't think we are considering it too seriously at this point. The idea was to examine if there were any systematic biases that the video parsing introduces. There is also some code that we will have to change as it relies on video parsing errors to detect when the worm is touching itself. At this point though we are not pursuing parsing of simulation video.

We had also mentioned improving the existing video extraction code for the real worms, as this might give us better data to work with for comparing to the simulation data. This is also not currently being pursued.

Finally, what we really need as an input is the worm contour, along with orientation information (head, tail, vulva). The skeleton can be derived from this information.

Jim

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[Mike Vella]

Excellent! I think it would be relatively straightforward to go from the sph data to a worm skeleton. I'm very excited that so much work has gone into this. Well done guys!

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