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mleiwe / PathologyRegistrationPipeline

A Project for the Merbl lab at Cornell. The aim is to create a registration pipeline whereby large .bif files of histological sections can be put in registration with an MRI template in order to view the anatomy in high resolution.
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MRI contrast adjustment #18

Open FlorianeSudre opened 4 days ago

FlorianeSudre commented 4 days ago

Can't assign myself to the issue for some reason. But I'm on it.

mleiwe commented 4 days ago

Let me also upload the whole atlas to the google drive for you. By the way could you create a .toml file for your libraries? I don't mind if you want to use poetry or something to make it more modern.

Also feel free to tag the branch you're working on here

FlorianeSudre commented 4 days ago

I saw the Johnson et al. atlas on the drive, thank you! At the moment I am using a virtual environment and I freeze the dependencies on a requirements.txt, would that be ok with you? I haven't migrated to poetry yet.

mleiwe commented 4 days ago

I haven't yet either. requirements.txt from a freeze is good for now. But it would be good to practice with a .yml or .toml eventually

FlorianeSudre commented 4 days ago

Working on this branch: https://github.com/mleiwe/PathologyRegistrationPipeline/tree/FS_EDA_v1