Dear colleagues,
A good FIB-SEM data stack can contain a few thousands pictures. It is very tricky and annoying process to segment them all manually. Which software do you use (real practical experience with big data) for such tasks?
Cheers,
Denis
Hi Denis Korneev and Andreas Müller,
You can also try Dragonfly (https://www.theobjects.com/dragonfly/index.html) from Object Research Systems, it is free for non commercial use.
Dragonfly has many segmentation tools from active shape to deep neural networks. The following video, (https://www.youtube.com/watch?v=1WVlskyuw94) is a deep learning tutorial.
Do not hesitate to contact me if you want more information.
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
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
For filters,FFT,contrast-Fiji
aligment and segmentation-MIB
http://mib.helsinki.fi/
for 3D and movie- Amira
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! :-)
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
Dear Andreas,
Thanks a lot. I use MIB now, but will try ilastik too.
Cheers,
Denis
Hi Denis Korneev and Andreas Müller,
You can also try Dragonfly (https://www.theobjects.com/dragonfly/index.html) from Object Research Systems, it is free for non commercial use.
Dragonfly has many segmentation tools from active shape to deep neural networks. The following video, (https://www.youtube.com/watch?v=1WVlskyuw94) is a deep learning tutorial.
Do not hesitate to contact me if you want more information.
Denis, Andreas, you might wanna give CDEEP3M a try
https://cdeep3m-stage.crbs.ucsd.edu/cdeep3m
Thanks Rafael Arrojo e Drigo and Nicolas Piché ! Sound both very interesting!
Dear Nicolas Piché and Rafael Arrojo e Drigo thank you very much for the useful links!
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