Re: Mito install

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Rick Giuly

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Sep 27, 2011, 2:09:36 PM9/27/11

to Sid Vijay, cyt...@googlegroups.com

Hi Sid,

First you need to have a training image stack and corresponding training
segmentation stack.

Examples are:
/ncmirdata1/rgiuly/neuropil/data
/ncmirdata1/rgiuly/neuropil/seg

(This example segmentation only exists at about 200-270, so ignore the
rest of the slices.)

Then you can process a particular data stack like
/ncmirdata1/rgiuly/neuropil/data or any other data that looks like it.
The data that you want to process is the "input" parameter to the script.

When the script is run, it uses the training data/segmentation to build
a classifier and then applies the classifier to the input to generate
output. The programs outputs several different things for diagnostic
reasons. The folder in the output that's good to look at for now is
voxelOutput/mitochondria/composite. It will show you a colorized image
with the detected mitochondria highlighted.

hope that helps!

-Rick

Sid Vijay wrote:
> Hey Rick,
>
> I think I've gotten cytoseg correctly installed. I'm trying to set up
> the segmentingmitochondria tutorial but I'm a little confused about the
> workflow. Would you mind describing the basic workflow?
>
> Sid

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