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Error when running rnascope_human on 3 channel z stack #16

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rahmas36 opened this issue Aug 17, 2022 · 0 comments
Open

Error when running rnascope_human on 3 channel z stack #16

rahmas36 opened this issue Aug 17, 2022 · 0 comments

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@rahmas36
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Hi, I am trying to run the rnascope_human script on a 3 channel z-stack czi file which contains a gene labeled in Opal 690 in Ch1, a gene labeled in Opal 570 in Ch2, and DAPI in Ch3. Every channel contains 37 z stacks. The script can read all 111 frames but gives 2 error messages at the end.

filename='/Users/samirrahman/Documents/MATLAB/dotdotdot-master/images/553_NEUROD1_CRISPRi_scrambled_63x_1.czi';
toolbox='/Users/samirrahman/Documents/MATLAB/dotdotdot-master/toolbox';
DAPI='Ch3';
LIP='';
DROP='';
addpath(genpath(toolbox))
rnascope_human(filename,toolbox,DAPI,LIP,DROP)
Reading Images: 1 of 111 Frames
Reading Images: 2 of 111 Frames
Reading Images: 3 of 111 Frames
Reading Images: 4 of 111 Frames
Reading Images: 5 of 111 Frames
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Reading Images: 111 of 111 Frames
extracted
{'ODye1'}
{'ODye2'}
{'ODye3'}

Elapsed time is 162.937864 seconds.
Undefined function 'std2' for input arguments of type 'double'.

Error in rnascope_human (line 75)
channel = imhmin(eval(channe_i),std2(eval(channe_i)));% suppress background noise in RNA scope channels.

What do these errors mean? Looking forward to your assistance.

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