These are chat archives for epnev/ca_source_extraction
Matlab implementation of a source extraction and spike inference algorithm for large scale calcium imaging data analysis, based on a constrained matrix factorization approach.
initialize_components.mIf you can modify the FISTA approach to give the outputs in that format then it should be easy to integrate with our framework. I'll be happy to incorporate these changes in our framework.
@epnev Thanks for your response. I am going to try out the large datasets.
About the error message in
run_pipeline.m, I get this as soon as I run the script:
>> run_pipeline Starting parallel pool (parpool) using the 'local' profile ... connected to 6 workers. The file was loaded successfully. Elapsed time : 0.172 s. Warning: File /media/jantine/Data/02_CaAnalysis/Epnev/ca_source_extraction/demoMovie_nr.h5already exists. Saving motion corrected file as/media/jantine/Data/02_CaAnalysis/Epnev/ca_source_extraction/demoMovie_nr_20170720T161950.h5 > In normcorre_batch (line 208) In run_pipeline (line 28) Template initialization complete. Error using shift_reconstruct (line 42) Matrix dimensions must agree. Error in normcorre_batch (line 260) parfor ii = 1:lY Error in run_pipeline (line 28) [M,shifts,template] = normcorre_batch(fullname,options_nonrigid,template);
Does this help? Or would you like to have more information?
@epnev I am trying out the
demo_CSHL2017_neurofinder.02.00.m and need the function
Undefined function or variable 'read_neurofinder'. Error in demo_CSHL2017_neurofinder_02_00 (line 17) Ycon = read_neurofinder(foldername,fullfile(foldername,'neurofinder0200.tif'));
Where can I find the function? I've been looking in the repo of
ca_source_extraction' and 'neurofinder but couldn't find it.