Johannes Friedrich

My new MacBook Pro with M1 chip and 16GB RAM arrived. The package-based as well as development mode install of CaImAn are both successful. The nosetests all succeed. The package-based...

That's indeed the case. In the package dir `file python` only outputs `python: Mach-O 64-bit executable x86_64`, whereas `file /usr/bin/python` yields ``` /usr/bin/python: Mach-O universal binary with 2 architectures: [x86_64:Mach-O...

@m-bellv, not sure I understand, do you already have a noisy temporal trace for each neuron, instead of a noisy fluorescence trace for each pixel? If you want to denoise...

Yes, that is rather normal if you do not set the temporal parameter `bas_nonneg` to `True`. `estimates.C-estimates.bl[:,None]` will always be non negative, but if `bas_nonneg=False` then `estimates.bl` can be negative,...

`esimates.S` is the deconvolved trace, `estimates.C` the denoised trace. To get the noisy raw trace you can add the residual, `estimates.C+estimates.R`. (Or solve the least squares problem `min_{C,f} |[A,b]*[C;f] -...

Apparently in your case `gSig` is an `int` but should be a tuple, list or array. When initializing the parameters, did you set `gSig = [4,4]` (line 166 in the...

20 frames is extremely short, usual data has 1000s. The `window` in `local_correlations_movie_offline` should be

Indeed, `gSig` seems quite large. Further, the threshold for `min_corr` determined using `caiman.utils.visualization.nb_inspect_correlation_pnr` might be too low because you use downscaling during the initialization (`tsub>1`, `ssub>1`). Whereas `min_pnr` is automatically...

Thanks Takashi for letting us know. I tried, and ran into the same issue using a fresh clone of the current master branch. Changing the environment.yml to force python==3.9 I...