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choosehappy / QuickAnnotator

An open-source digital pathology based rapid image annotation tool
BSD 3-Clause Clear License
74 stars 27 forks source link

How to download the annotations with a unique integer for each individual nucleus #27

Open sanomamoudou opened 2 years ago

sanomamoudou commented 2 years ago

Hello, Thank you for this amazing tool. I want to have an instance map for my training annotation, eg: a unique integer for each individual nucleus. How can I do this ?? or the tool don't this option ??

Thanks in advance

choosehappy commented 2 years ago

sorry, i'm not sure i totally understand your question, but if you look here:

https://github.com/choosehappy/PatchSorter/wiki/Frequently-Asked-Questions

i think you'll see that what you're referring to is called an "indexed mask", and that patchsorter does support these? have you tried using this functionality?

On Mon, Jul 25, 2022 at 2:16 PM sanomamoudou @.***> wrote:

Hello, Thank you for this amazing tool. I want to have an instance map for my training annotation, eg: a unique integer for each individual nucleus. How can I do this ?? or the tool don't this option ??

Thanks in advance

— Reply to this email directly, view it on GitHub https://github.com/choosehappy/QuickAnnotator/issues/27, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACJ3XTFGUJRVJHFQTRSAW2LVV2ASPANCNFSM54SCISXQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

sanomamoudou commented 2 years ago

Hi @choosehappy. Thank you for your feedback. Yes, exactly I am talking about "indexed mask". I thought it was possible to annotate and download our masks in this format with QuickAnnotator. But I haven't tried yet PatchSorter, I'll test this functionality on PatchSorter. Thank you!

choosehappy commented 2 years ago

Ah, sorry, i understand your question better now

Currently, QuickAnnotator doesn't provide direct support for this since i just realized we don't have a way of differentiating two objects that are touching each other in the UI.

as a result, the outputs are binary masks, as i'm sure you've noticed

if you want to convert those to indexed images, and if the objects are separated, you can produce an index image easily with 1 line of python code:

https://scikit-image.org/docs/stable/api/skimage.measure.html#skimage.measure.label

On Fri, Jul 29, 2022 at 10:23 AM sanomamoudou @.***> wrote:

Hi @choosehappy https://github.com/choosehappy. Thank you for your feedback. Yes, exactly I am talking about "indexed mask". I thought it was possible to annotate and download our masks in this format with QuickAnnotator. But I haven't tried yet PatchSorter, I'll test this functionality on PatchSorter. Thank you!

— Reply to this email directly, view it on GitHub https://github.com/choosehappy/QuickAnnotator/issues/27#issuecomment-1199010608, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACJ3XTDLUYRMHLB7C2ZNIDTVWOIH3ANCNFSM54SCISXQ . You are receiving this because you were mentioned.Message ID: @.***>

sanomamoudou commented 2 years ago

Ok got it thank you !