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Problem with reading CZI file #15

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rahmas36 opened this issue Aug 11, 2022 · 0 comments
Open

Problem with reading CZI file #15

rahmas36 opened this issue Aug 11, 2022 · 0 comments

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@rahmas36
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Hi, I have a CZI file with 4 channels (Cy5, Cy3, GFP, DAPI), and each channel has 37 z-stacks. I am trying to read this file with the rnascope_human script in the dotdotdot Toolbox directory. I received an error message about not having enough input arguments:

filename = '/Users/samirrahman/Documents/MATLAB/dotdotdot-master/images/NEUROD1_CUX2_SATB2_63x_200_ms_1.czi';
toolbox = '/Users/samirrahman/Documents/MATLAB/dotdotdot-master/toolbox';
rnascope_human(filename, toolbox)
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Not enough input arguments.

Error in rnascope_human (line 29)
if strcmp(O(i),DAPI)

Do I specify the name of every channel. For example, in my case DAPI is channel 4, the gene CUX2 is in channel 1, NEUROD1 is in channel 2, SATB2 is in channel 3. Should I load maximum projections of every channel or can the script read in 3D?

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