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Cytoseg

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The goal of the Cytoseg project is to produce a tool for automatic segmentation of 3D biological datasets, with emphasis on 3D electron microscopy. The project is written in Python and uses the completely open source pythonxy platform (which includes scipy and ITK image processing tools). Cytoseg is currently in beta stage.

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4/9/13

Fwd: Re: NodeDoesNotExist2

Hi Kurt, kurt weiss wrote: > Okay, I think I get it. The distance you look in 2-D depends largely

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Fwd: Re: NodeDoesNotExist2

Hi Kurt, kurt weiss wrote: > Okay, I think I get it. The distance you look in 2-D depends largely

4/9/13

4/8/13

Re: NodeDoesNotExist

Hi Kurt, This line gives you v: v = volume[point[0]-size:point[0]+size,point[1]-size:point[1]+size,

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Re: NodeDoesNotExist

Hi Kurt, This line gives you v: v = volume[point[0]-size:point[0]+size,point[1]-size:point[1]+size,

4/8/13

Rick Giuly, kurt weiss3

4/2/13

Adding features for voxel classification

Hi Kurt, (1) This section is the one that I was referring to. Note: It's the one that's *not*

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Adding features for voxel classification

Hi Kurt, (1) This section is the one that I was referring to. Note: It's the one that's *not*

4/2/13

3/5/13

Error should be fixed

Hi Kurt, the error should now be fixed. New version is online. Changed this file only: http://code.

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Error should be fixed

Hi Kurt, the error should now be fixed. New version is online. Changed this file only: http://code.

3/5/13

3/2/13

Re: cytoseg questions

Hi Kurt, Interesting questions kurt weiss wrote: > Hi Rick, > > Thanks for the update on

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Re: cytoseg questions

Hi Kurt, Interesting questions kurt weiss wrote: > Hi Rick, > > Thanks for the update on

3/2/13

2/28/13

Training data, picking and choosing examples

Hi Alex and Kurt, If you're using the contour processing stage in Cytoseg, there is a caveat with

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Training data, picking and choosing examples

Hi Alex and Kurt, If you're using the contour processing stage in Cytoseg, there is a caveat with

2/28/13

2/7/13

Re: general question on training sets

Good question. My experience is this: I use (A), within single datasets. I prefer to normalize each

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Re: general question on training sets

Good question. My experience is this: I use (A), within single datasets. I prefer to normalize each

2/7/13

1/16/13

How to change minimum object size in cytoseg

Hi Kurt. There's no command line parameter to adjust the minimum size yet, but if you edit the

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How to change minimum object size in cytoseg

Hi Kurt. There's no command line parameter to adjust the minimum size yet, but if you edit the

1/16/13

11/13/12

Re: cytoseg output

Hi Kurt, glad to hear you're getting nice results! Right now you're looking at the "

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Re: cytoseg output

Hi Kurt, glad to hear you're getting nice results! Right now you're looking at the "

11/13/12

11/2/12

Training segmentation and objects besides mitochondria

Hi Kurt, More good questions > Is it necessary to go to this level of detail on each and every

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Training segmentation and objects besides mitochondria

Hi Kurt, More good questions > Is it necessary to go to this level of detail on each and every

11/2/12

11/2/12

Re: Autoseg test

The last one in the list is the one you want to use, it's the "total" -Rick On 11/02/

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Re: Autoseg test

The last one in the list is the one you want to use, it's the "total" -Rick On 11/02/

11/2/12

11/1/12

Re: cytoseg on jane

Hi Alex, please go ahead and download cytoseg again, because I made some updates. You can redo the

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Re: cytoseg on jane

Hi Alex, please go ahead and download cytoseg again, because I made some updates. You can redo the

11/1/12

10/31/12

Re: CytoSeg help

Hi Kurt, Got it, this means that the process is running OK. The issue is just accuracy. What you'

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Re: CytoSeg help

Hi Kurt, Got it, this means that the process is running OK. The issue is just accuracy. What you'

10/31/12

7/12/12

Re: Submitting autoseg jobs on SLASH portal

OK, I see what you're asking now. You'll need a closed contour. I usually end up making the

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Re: Submitting autoseg jobs on SLASH portal

OK, I see what you're asking now. You'll need a closed contour. I usually end up making the

7/12/12

6/26/12

Fwd: Re: Run_cytoseg_on_cluster

-------- Original Message -------- Subject: Re: Run_cytoseg_on_cluster Date: Tue, 26 Jun 2012 11:40:

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Fwd: Re: Run_cytoseg_on_cluster

-------- Original Message -------- Subject: Re: Run_cytoseg_on_cluster Date: Tue, 26 Jun 2012 11:40:

6/26/12

9/27/11

Re: Mito install

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

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Re: Mito install

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

9/27/11

7/17/10

Re: Cytoseg on cluster0 update

Hi, I think it looks good, but I'd need to see the block that you are using for the corresponding

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Re: Cytoseg on cluster0 update

Hi, I think it looks good, but I'd need to see the block that you are using for the corresponding

7/17/10

2/10/10

Status update for Cytoseg

Automatic Segmentation Using two major stages: (1) A denoising stage that acts on local patches - it

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Status update for Cytoseg

Automatic Segmentation Using two major stages: (1) A denoising stage that acts on local patches - it

2/10/10

12/16/09

Hi Willy, There's a script here that should work: cytoseg:~/cytoseg-read-only/cytoseg/testing You

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Hi Willy, There's a script here that should work: cytoseg:~/cytoseg-read-only/cytoseg/testing You

12/16/09

5/2/09

Re: Sample Code Questions: \cytoseg\load_stack.py

The python example scripts (which both itk and opencv have many of) are a good place to start. For

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Re: Sample Code Questions: \cytoseg\load_stack.py

The python example scripts (which both itk and opencv have many of) are a good place to start. For

5/2/09

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