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Error trying to run RAPID #1
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Did you ever figure out the problem? |
Sorry, no
…On Mon, Nov 20, 2023, 3:36 PM Justin Smith ***@***.***> wrote:
Did you ever figure out the problem?
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Hi everyone, I have run into the same error when trying to run RAPID for our lab’s CODEX images, and I’ve been trying to troubleshoot the script for the past 2 months. This particular error occurs because “makeMosaic.m” looks for a file called “reg(#)_cycle(#)_global-positions-0.txt” within the output folder but can’t find it. I have side-stepped this issue by running the MIST stitching plugin manually for each cycle. In my case, I have a 6 x 9 grid, so the Deconvolution script in Module 1 generated 54 tiles within each of my “/1_deconv_stitch/cycle(#)/” directories. Tab 1: Input Tab 2: Output Pixel Size Metadata: enter as needed. Mine is in nanometers, 377.0 (x) by 377.0 (y) Tab 3: Subgrid Tab 4: Advanced Other Advanced Parameters: leave all UNchecked Then click Begin Stitching. After this process is finished, you will have 5 new .txt files in your "1_deconv_stitch\cycle(#)" directory. You will need to repeat the MIST Stitching process for each Cycle. This should be relatively fast at this step since you have set up most of the stitching parameters. etc. Once each Cycle folder has a global positions file, you can run Module 2 in RAPID.m. This time, makeMosaic.m should work as intended. You will end up with a "_montage.tif" file within each Cycle folder after this module is finished. However, I was using the “multipoint” module on our Keyence microscope, so I had to edit the script of driftCompensate_par.m as well because the current multipoint script tries to overlay "tile_1.tif" from Cycles 2-n with the "_montage.tif" image from Cycle 1. If you are using the memopoint module, I think you won’t have this problem. I also had to add the argument “mode” to the function in Line 13 of driftCompensate_par.m in order to get this script to run properly as well. That is, Line 13 now reads as follows: Make sure to change this in Line 91 of the RAPID.m script as well. Anyway, this is the only work-around I have found. It's a bit time-intensive depending on the number of regions/cycles you have, but it does work. I am trying to figure out why MATLAB is having issues running the MIST plugin from Fiji. All other Fiji/ImageJ functions are working fine in the context of Miji (e.g. the genHyperstack.m script runs fine). “ImageJ 1.54f; Java 1.8.0_202 [64-bit]; Windows 10 10.0; 316MB of 26358MB (1%) java.lang.NoSuchFieldError: COMPRESSION_ZLIB It seems that maybe the ZLIB compression option within the MIST plugin, found in the Compression drop-down menu from the Output tab, is causing some kind of error in the initialization of the Plugin. |
I am not sure what is wrong..
Below are the logs:
Start deconvolution...
Warning: File: deconv_par.m Line: 40 Column: 13
The temporary variable 'im_folder_name' will be cleared at the beginning of each iteration of the parfor-loop. If 'im_folder_name' is used before it is set, a runtime error will
occur. For more information, see Parallel for Loops in MATLAB, "Uninitialized Temporaries".
MIJ 1.3.9: Matlab to ImageJ Interface
More Info: http://bigwww.epfl.ch/sage/soft/mij/
Help: MIJ.help
JVM> 1.3.9
JVM> Version: 1.8.0_202
JVM> Total amount of memory: 1293312 Kb
JVM> Amount of free memory: 276734 Kb
ImageJ> Version:1.53i
ImageJ> Memory:1039MB of 26427MB (3%)
ImageJ> Directory plugins: C:\Users\kchu\Fiji.app\plugins
ImageJ> Directory macros: C:\Users\kchu\Fiji.app\macros
ImageJ> Directory luts: C:\Users\kchu\Fiji.app\luts
ImageJ> Directory image: Not specified
ImageJ> Directory imagej: C:\Users\kchu\Fiji.app
ImageJ> Directory startup: C:\Users\kchu\Fiji.app
ImageJ> Directory home: C:\Users\kchu\
Status> ImageJ is running.
generating stitching positions: reg4...
generating stitching positions: cyc1...
generating stitching positions: cyc2...
generating stitching positions: cyc3...
generating stitching positions: cyc4...
generating stitching positions: cyc5...
generating stitching positions: cyc6...
generating stitching positions: cyc7...
generating stitching positions: cyc8...
generating stitching positions: cyc9...
generating stitching positions: cyc10...
generating stitching positions: cyc11...
generating stitching positions: cyc12...
generating stitching positions: cyc13...
generating stitching positions: cyc14...
generating stitching positions: cyc15...
generating stitching positions: cyc16...
generating stitching positions: cyc17...
generating stitching positions: cyc18...
generating stitching positions: cyc19...
generating stitching positions: cyc20...
ImageJ instance ended cleanly
Making mosaics...
Region 4 mosaics
Cycle 1 mosaic
Error using feof
Invalid file identifier. Use fopen to generate a valid file identifier.
Error in load_csv_file_into_cell_array (line 31)
while ~feof(fh)
Error in makeMosaic (line 21)
cell_array = load_csv_file_into_cell_array(global_pos_path);
Error in RAPID_0097_ver2 (line 96)
makeMosaic(path_output,reg_range,cyc_range);
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