Which software do you use for biological FIB-SEM data segmentation?

Karthika .P

Summary of Interactive Segmentation Tools

1) For 2D images Human guided scribble based interactive segmentation tool.

Links:

http://web.archive.org/web/20110825021314/http://kspace.cdvp.dcu.ie/public/interactive-segmentation/

http://www.youtube.com/watch?v=efUh0zcpsXc

2) 3D Interactive Segmentation Tool FIJI

Links:

http://132.187.25.13/ij3d/?page=IntSeg_3D&category=Extensions

http://fiji.sc (or) http://rsbweb.nih.gov/ij/

http://www.youtube.com/watch?v=IR_1n24qCaU

3) 3D-2D Interactive Segmentation Tool TurtleSeg

Links:

http://www.turtleseg.org/

http://www.youtube.com/watch?v=TBEoJxj-EdQ

4) 3D-2D Interactive Segmentation Tool FIJI

Links:

http://132.187.25.13/home/?category=Download&page=SegmentationEditor

http://fiji.sc (or) http://rsbweb.nih.gov/ij/

http://www.youtube.com/watch?v=tC-b-BFq6jk

5) For 3D-2D images MITK Interactive segmentation tool

Links:

http://www.mitk.org/Interactive_segmentation

http://www.youtube.com/watch?v=hEZsQsTxMlo

6) GIMP - GNU Image Manipulation Program (Open source alternative to Adobe Photoshop)

http://docs.gimp.org/en/gimp-tools-selection.html

http://www.gimp.org/

http://www.youtube.com/watch?v=p0VbK6MjEv8

Denis Korneev

Hi Karthika

Thanks for the useful list of software. Did you use them all? I meant an answer from personal practice like "I prefer software ABCDE, because it works very well for membranes and cell organelles recognition, it has a lot of adjustable parameters and works pretty stable with big pictures...". It is just a dream, I know :)

Cheers,

Denis

Anya Vainshtein

For filters,FFT,contrast-Fiji

aligment and segmentation-MIB

http://mib.helsinki.fi/

for 3D and movie- Amira

Denis Korneev

Thanks Anya. Yep. I use Fiji for filtering and stack registration, then Amira for 3d. Segmentation is the most serious issue, last time I have segmented 800 pictures manually, that was terrible! :-)

Andreas Müller

Dear Denis,

I recently started using ilastik ( https://www.ilastik.org/ ) for segmentation and I'm pretty happy with it.

You just need to do a little bit of annotation and get a reasonable result.

I started with autocontext for pixel classification followed by object classification.

Best,

Andreas

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