search

LieberInstitute / dotdotdot

Example vignette for dotdotdot software
GNU Affero General Public License v3.0
18 stars 11 forks source link

Problem with reading CZI file #15

Open rahmas36 opened 2 years ago

rahmas36 commented 2 years ago

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) Reading Images: 1 of 148 Frames Reading Images: 2 of 148 Frames Reading Images: 3 of 148 Frames Reading Images: 4 of 148 Frames Reading Images: 5 of 148 Frames Reading Images: 6 of 148 Frames Reading Images: 7 of 148 Frames Reading Images: 8 of 148 Frames Reading Images: 9 of 148 Frames Reading Images: 10 of 148 Frames Reading Images: 11 of 148 Frames Reading Images: 12 of 148 Frames Reading Images: 13 of 148 Frames Reading Images: 14 of 148 Frames Reading Images: 15 of 148 Frames Reading Images: 16 of 148 Frames Reading Images: 17 of 148 Frames Reading Images: 18 of 148 Frames Reading Images: 19 of 148 Frames Reading Images: 20 of 148 Frames Reading Images: 21 of 148 Frames Reading Images: 22 of 148 Frames Reading Images: 23 of 148 Frames Reading Images: 24 of 148 Frames Reading Images: 25 of 148 Frames Reading Images: 26 of 148 Frames Reading Images: 27 of 148 Frames Reading Images: 28 of 148 Frames Reading Images: 29 of 148 Frames Reading Images: 30 of 148 Frames Reading Images: 31 of 148 Frames Reading Images: 32 of 148 Frames Reading Images: 33 of 148 Frames Reading Images: 34 of 148 Frames Reading Images: 35 of 148 Frames Reading Images: 36 of 148 Frames Reading Images: 37 of 148 Frames Reading Images: 38 of 148 Frames Reading Images: 39 of 148 Frames Reading Images: 40 of 148 Frames Reading Images: 41 of 148 Frames Reading Images: 42 of 148 Frames Reading Images: 43 of 148 Frames Reading Images: 44 of 148 Frames Reading Images: 45 of 148 Frames Reading Images: 46 of 148 Frames Reading Images: 47 of 148 Frames Reading Images: 48 of 148 Frames Reading Images: 49 of 148 Frames Reading Images: 50 of 148 Frames Reading Images: 51 of 148 Frames Reading Images: 52 of 148 Frames Reading Images: 53 of 148 Frames Reading Images: 54 of 148 Frames Reading Images: 55 of 148 Frames Reading Images: 56 of 148 Frames Reading Images: 57 of 148 Frames Reading Images: 58 of 148 Frames Reading Images: 59 of 148 Frames Reading Images: 60 of 148 Frames Reading Images: 61 of 148 Frames Reading Images: 62 of 148 Frames Reading Images: 63 of 148 Frames Reading Images: 64 of 148 Frames Reading Images: 65 of 148 Frames Reading Images: 66 of 148 Frames Reading Images: 67 of 148 Frames Reading Images: 68 of 148 Frames Reading Images: 69 of 148 Frames Reading Images: 70 of 148 Frames Reading Images: 71 of 148 Frames Reading Images: 72 of 148 Frames Reading Images: 73 of 148 Frames Reading Images: 74 of 148 Frames Reading Images: 75 of 148 Frames Reading Images: 76 of 148 Frames Reading Images: 77 of 148 Frames Reading Images: 78 of 148 Frames Reading Images: 79 of 148 Frames Reading Images: 80 of 148 Frames Reading Images: 81 of 148 Frames Reading Images: 82 of 148 Frames Reading Images: 83 of 148 Frames Reading Images: 84 of 148 Frames Reading Images: 85 of 148 Frames Reading Images: 86 of 148 Frames Reading Images: 87 of 148 Frames Reading Images: 88 of 148 Frames Reading Images: 89 of 148 Frames Reading Images: 90 of 148 Frames Reading Images: 91 of 148 Frames Reading Images: 92 of 148 Frames Reading Images: 93 of 148 Frames Reading Images: 94 of 148 Frames Reading Images: 95 of 148 Frames Reading Images: 96 of 148 Frames Reading Images: 97 of 148 Frames Reading Images: 98 of 148 Frames Reading Images: 99 of 148 Frames Reading Images: 100 of 148 Frames Reading Images: 101 of 148 Frames Reading Images: 102 of 148 Frames Reading Images: 103 of 148 Frames Reading Images: 104 of 148 Frames Reading Images: 105 of 148 Frames Reading Images: 106 of 148 Frames Reading Images: 107 of 148 Frames Reading Images: 108 of 148 Frames Reading Images: 109 of 148 Frames Reading Images: 110 of 148 Frames Reading Images: 111 of 148 Frames Reading Images: 112 of 148 Frames Reading Images: 113 of 148 Frames Reading Images: 114 of 148 Frames Reading Images: 115 of 148 Frames Reading Images: 116 of 148 Frames Reading Images: 117 of 148 Frames Reading Images: 118 of 148 Frames Reading Images: 119 of 148 Frames Reading Images: 120 of 148 Frames Reading Images: 121 of 148 Frames Reading Images: 122 of 148 Frames Reading Images: 123 of 148 Frames Reading Images: 124 of 148 Frames Reading Images: 125 of 148 Frames Reading Images: 126 of 148 Frames Reading Images: 127 of 148 Frames Reading Images: 128 of 148 Frames Reading Images: 129 of 148 Frames Reading Images: 130 of 148 Frames Reading Images: 131 of 148 Frames Reading Images: 132 of 148 Frames Reading Images: 133 of 148 Frames Reading Images: 134 of 148 Frames Reading Images: 135 of 148 Frames Reading Images: 136 of 148 Frames Reading Images: 137 of 148 Frames Reading Images: 138 of 148 Frames Reading Images: 139 of 148 Frames Reading Images: 140 of 148 Frames Reading Images: 141 of 148 Frames Reading Images: 142 of 148 Frames Reading Images: 143 of 148 Frames Reading Images: 144 of 148 Frames Reading Images: 145 of 148 Frames Reading Images: 146 of 148 Frames Reading Images: 147 of 148 Frames Reading Images: 148 of 148 Frames 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?