investigate pika ROI classifier - Githubissues

AllenNeuralDynamics / aind-ophys-utils

Repo for Ophys utils

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investigate pika ROI classifier #11

Open arielleleon opened 1 year ago

arielleleon commented 1 year ago

[ ] what are the inputs & outputs?
[ ] how does it work? what are the pros & cons?
[ ] how does it perform on current data?
[ ] what metrics do we want to track to evaluate performance?

Prior work on this:

https://github.com/AllenInstitute/LearningmFISHTask1A_data_validation/issues/32 https://github.com/AllenInstitute/LearningmFISHTask1A_data_validation/issues/34 https://github.com/AllenInstitute/LearningmFISHTask1A_data_validation/issues/11

MJD notes:

here are the slides describing the problems and Pika ROI classifier solution: https://alleninstitute-my.sharepoint.com/:p:/g/personal/michael_wang_alleninstitute_org/EdZX81Ffj9JGkWvmvN45XAoBxT6c_4Dd1IKn5M87bof2Gg?e=hCDMai&CID=BC5CAEB5-1DC1-4A82-B5EF-777BA3EF0CD0&wdLOR=cE38AACAC-3C25-4AE8-9FAF-1D9F5F9435F5
labeling app slides: https://alleninstitute.sharepoint.com/sites/Pika/Shared%20Documents/Forms/AllItems.aspx?id=%2Fsites%2FPika%2FShared%20Documents%2FCell%20Segmentation%202021%2Flabeling%5Fapp%5Finstructions%2Epdf&parent=%2Fsites%2FPika%2FShared%20Documents%2FCell%20Segmentation%202021&p=true&wdLOR=cE503F683%2DCA0C%2D4598%2D8F76%2D295680040A32&ct=1689281348541&or=Outlook%2DBody&cid=F300137C%2D8FC7%2D4A73%2D8A4C%2D4C9C6B7CC5CD&ga=1
Note: this was for the challenging deepscope dataset that had low SNR, but no crosstalk (multiple planes)

Model inputs

matchings commented 12 months ago

Still need to compare this implementation of ROI classification versus other available methods