Bugs in exp.separate

[Hanbing1999]

Hi everyone! I'm using using FISSA with CNMF from MATLAB. At first, I tested the example data (within fissa_master), and all steps are correct. But when I using my own data, exp.seprate(redo_prep = True) reports ValueError: A LinearRing must have at least 3 coordinate tuples. And details are provided in the following figures. Since I'm totally new to Python, I'm not sure how to deal with it.

Thanks for your time!

[swkeemink]

It appears that there is something about the cNMF detected ROIs that is no compatible with FISSA. Can you give some details about how you run cNMF, what data you extract, and how you plug them into FISSA?

[Hanbing1999]

It appears that there is something about the cNMF detected ROIs that is no compatible with FISSA. Can you give some details about how you run cNMF, what data you extract, and how you plug them into FISSA?

Hi, I use run_pipeline.m to analyze a series of motion-corrected tif files and save the results as a struct.

dat.Coor = Coor;
dat.A = A_keep;
F_df = num2cell(F_dff,2);% 2 cut through lines ; while 1 represents cut through rows 
dat.F_df = F_df;
save('D:\project\data\SM75-D1-Cre_test2\20190506\CNMF\sequence\cNMFdata.mat','dat')

Then I load FISSA and holoviews, and load the data:

cNMFdata = loadmat('D://project//data//SM75-D1-Cre_test2//20190506//CNMF//sequence//cNMFdata.mat')['dat']
F_df = cNMFdata['F_df'][0, 0]
Coor = cNMFdata['Coor'][0, 0]

And actually, I can plot the lines surrounding each of the ROIs.

[swkeemink]

From the plotting of the regions of interest it looks like the algorithm found a lot of extremely small ROIs, which might only consist of two coordinates. cNMF might have some setting to get rid of some of these, or you can try to do that by hand.

You could also check that by seeing the length of each Coor[i, 0].

Which version of cNMF are you using?