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LieberInstitute / dotdotdot

Example vignette for dotdotdot software
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Error when running rnascope_human on 3 channel z stack #16

Open rahmas36 opened 2 years ago

rahmas36 commented 2 years ago

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 Reading Images: 6 of 111 Frames Reading Images: 7 of 111 Frames Reading Images: 8 of 111 Frames Reading Images: 9 of 111 Frames Reading Images: 10 of 111 Frames Reading Images: 11 of 111 Frames Reading Images: 12 of 111 Frames Reading Images: 13 of 111 Frames Reading Images: 14 of 111 Frames Reading Images: 15 of 111 Frames Reading Images: 16 of 111 Frames Reading Images: 17 of 111 Frames Reading Images: 18 of 111 Frames Reading Images: 19 of 111 Frames Reading Images: 20 of 111 Frames Reading Images: 21 of 111 Frames Reading Images: 22 of 111 Frames Reading Images: 23 of 111 Frames Reading Images: 24 of 111 Frames Reading Images: 25 of 111 Frames Reading Images: 26 of 111 Frames Reading Images: 27 of 111 Frames Reading Images: 28 of 111 Frames Reading Images: 29 of 111 Frames Reading Images: 30 of 111 Frames Reading Images: 31 of 111 Frames Reading Images: 32 of 111 Frames Reading Images: 33 of 111 Frames Reading Images: 34 of 111 Frames Reading Images: 35 of 111 Frames Reading Images: 36 of 111 Frames Reading Images: 37 of 111 Frames Reading Images: 38 of 111 Frames Reading Images: 39 of 111 Frames Reading Images: 40 of 111 Frames Reading Images: 41 of 111 Frames Reading Images: 42 of 111 Frames Reading Images: 43 of 111 Frames Reading Images: 44 of 111 Frames Reading Images: 45 of 111 Frames Reading Images: 46 of 111 Frames Reading Images: 47 of 111 Frames Reading Images: 48 of 111 Frames Reading Images: 49 of 111 Frames Reading Images: 50 of 111 Frames Reading Images: 51 of 111 Frames Reading Images: 52 of 111 Frames Reading Images: 53 of 111 Frames Reading Images: 54 of 111 Frames Reading Images: 55 of 111 Frames Reading Images: 56 of 111 Frames Reading Images: 57 of 111 Frames Reading Images: 58 of 111 Frames Reading Images: 59 of 111 Frames Reading Images: 60 of 111 Frames Reading Images: 61 of 111 Frames Reading Images: 62 of 111 Frames Reading Images: 63 of 111 Frames Reading Images: 64 of 111 Frames Reading Images: 65 of 111 Frames Reading Images: 66 of 111 Frames Reading Images: 67 of 111 Frames Reading Images: 68 of 111 Frames Reading Images: 69 of 111 Frames Reading Images: 70 of 111 Frames Reading Images: 71 of 111 Frames Reading Images: 72 of 111 Frames Reading Images: 73 of 111 Frames Reading Images: 74 of 111 Frames Reading Images: 75 of 111 Frames Reading Images: 76 of 111 Frames Reading Images: 77 of 111 Frames Reading Images: 78 of 111 Frames Reading Images: 79 of 111 Frames Reading Images: 80 of 111 Frames Reading Images: 81 of 111 Frames Reading Images: 82 of 111 Frames Reading Images: 83 of 111 Frames Reading Images: 84 of 111 Frames Reading Images: 85 of 111 Frames Reading Images: 86 of 111 Frames Reading Images: 87 of 111 Frames Reading Images: 88 of 111 Frames Reading Images: 89 of 111 Frames Reading Images: 90 of 111 Frames Reading Images: 91 of 111 Frames Reading Images: 92 of 111 Frames Reading Images: 93 of 111 Frames Reading Images: 94 of 111 Frames Reading Images: 95 of 111 Frames Reading Images: 96 of 111 Frames Reading Images: 97 of 111 Frames Reading Images: 98 of 111 Frames Reading Images: 99 of 111 Frames Reading Images: 100 of 111 Frames Reading Images: 101 of 111 Frames Reading Images: 102 of 111 Frames Reading Images: 103 of 111 Frames Reading Images: 104 of 111 Frames Reading Images: 105 of 111 Frames Reading Images: 106 of 111 Frames Reading Images: 107 of 111 Frames Reading Images: 108 of 111 Frames Reading Images: 109 of 111 Frames Reading Images: 110 of 111 Frames 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.