Organoids (Cells) Segmentation tools

Dear People

I am trying to perform the segmentation, labeling, and detection of cells nucleus using Ilastik but it seems that I can’t get the results I want due to different problems with this tool, one of them is that it stops responding randomly and is not making the segmentation of the organoids in a way I do not have to do a lot of correction after… My question is, do you know any image segmentation and annotation tool that can give a good performance and it can be used in Windows 10?

Thanks
Xareni :smiley:

hi
@xgalindo
Please post an image so that we can test.

Yes, it would be important to at least mention the imaging modality and whether the images are 2D,3D, 4D etc.

Dear Mathew and Research_Associate

thank you very much for you answers, sadly the forum do not allow me to add my files, but if you can send me your emails I will be happy to send them to you asap

Hi @xgalindo,
depending on how large the images are you can share them temporarily using Firefox Send (supports 1GB without the need to create an account)

Dear all

thank you for your advices, here is the link to the data by wetransfer and firefox send transfer. thank you for your help again

I was looking back through posts and and realized I didn’t respond, but I found that our ITS policy blocks me from both wetransfer and firefox send. :frowning:

thank you for your keep and eye in my comment, here I send you a google drive link with an example of the data I need to annotate

1 Like

Finally remembered to download this at home, am blocked at work. In the images you hosted, the top border looks fairly consistent, and you might be able to manually draw it once and then apply the same border to all similar images. There has also been talk somewhere about a Hough transform to find lines.


http://imagej.1557.x6.nabble.com/Hough-transform-problem-Edge-detection-td5010786.html