[Insight-users] Performing manual segmentation of cell images

[Kristen Zygmunt]

Hi Kevin,
   I can recommend Seg3D (seg3d.org) which has a concept of layers to manage different segmentations.  It's built on top of ITK and uses a number of ITK segmentation and processing filters.  (Disclosure:  I work at SCI and have helped maintain / develop Seg3D).

-Kris


> Date: Sat, 30 Nov 2013 13:24:37 +0000
> From: Kevin Keraudren <kevin.keraudren10 at imperial.ac.uk>
> Subject: [Insight-users] Performing manual segmentation of cell images
> To: insight-users at itk.org
> Message-ID: <5299E715.2040103 at imperial.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi,
> 
> I would like to manually segment a few cell images in order to evaluate 
> an automated segmentation (for instance trace the cell boundaries and 
> the contour of the nuclei).
> 
> I usually do manual segmentations with ITK-snap on medical images, not 
> microscopy images, but I think it is overkill for PNG/TIFF images, and 
> not appropriate to handle classes: I would like to have the cytoplasm 
> and the nuclei classes, and assign labels of the form cytoplasm-1, 
> cytoplasm-2, cytoplasm-3,... and nuclei-1, nuclei-2, nuclei-3.
> For my application, I would have more classes than just cytoplasm and 
> nuclei.
> 
> Would you know of a more appropriate program for this kind of manual 
> segmentation? In my mind it would be a tool that allow you to segment 
> the image with layers, as the layers of Photoshop or GIMP, and each 
> layer would correspond to a class.
> 
> Thanks a lot for your help,
> 
> Kind regards,
> 
> Kevin
> 
> 
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