Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
Right now it's a bit involved to take neurons that have been externally detected and bring them into Caiman. We have a notebook to do it, but it needs some love.
Ideally there should be a clear path to import ROIs defined in Cellpose or ImageJ, with that clear path not requiring any work in python (if people export ROIs to an image stack, we should make Caiman functions to import that image stack - it is not good enough to just instruct people how to do this kind of thing with numpy). Notebooks should also demonstrate this kind of thing clearly.
Right now it's a bit involved to take neurons that have been externally detected and bring them into Caiman. We have a notebook to do it, but it needs some love.
Ideally there should be a clear path to import ROIs defined in Cellpose or ImageJ, with that clear path not requiring any work in python (if people export ROIs to an image stack, we should make Caiman functions to import that image stack - it is not good enough to just instruct people how to do this kind of thing with numpy). Notebooks should also demonstrate this kind of thing clearly.