search

AI4SCR / ATHENA

BSD 3-Clause "New" or "Revised" License
30 stars 6 forks source link

Creating masks #1

Open johnyaku opened 2 years ago

johnyaku commented 2 years ago

Thank you for making a very interesting tool.

I've been working through the tutorial and noticed that the datasets already include segmentation masks. Can you provide advice on how to create masks in the first place? Squidpy, perhaps? Or maybe ImageJ or QuPath? Feel free to point to external references if that is easier than explaining here.

Thanks again.

adrianomartinelli commented 2 years ago

Hi! I did not explore the available tools in detail yet but as you pointed out squidpy is an option or maybe steinbock could be a good place to start? I think it also depends a bit on what kind of data you have...

Best, Adriano

johnyaku commented 2 years ago

Hi Adriano. Thanks for the tip. Our data is eleven-channel mIF