Re: Performing manual segmentation

Posted by Jerome Mutterer-3 on Dec 02, 2013; 9:12pm
URL: http://imagej.273.s1.nabble.com/Performing-manual-segmentation-tp5005745p5005781.html

Hi Kevin,

You could take advantage of the recent possibility to assign properties to
ROIs in ImageJ 1.48h.

I put together a simple test macro that does this. You can get it at:
https://gist.github.com/mutterer/7758228#file-roiclassestest-ijm
and adapt it to your needs. It just assigns a custom property and a stroke
color to the active ROI, and pushes it to the ROI manager. Then you can
select ROIs by keyword, which could be a starting point for your manual
segmentation analysis.

I recorded a small video about how to use it at:
http://youtu.be/RlhG23xPEbg

Sincerely,
Jerome



On 30 November 2013 14:22, Kevin Keraudren <[hidden email]
> wrote:

> 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.
>
> Could I use ImageJ for this? Otherwise would you know of an 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
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html