Problem tiling images from IFC in MATLAB

cellprofiler

#1

MATLAB is randomly having trouble tiling images obtained by IFC. I’m using the script uploaded to your website and haven’t made changes to it. I’m running the script found in the folder “MATLAB_tiling_without_GUI” in windows 10 and MATLAB 2018a. It works fine in most cases. But about 3/10 samples I get the following error…

cif_image_tiling
log4j:WARN No appenders could be found for logger (loci.formats.ClassList).
log4j:WARN Please initialize the log4j system properly.
Exporting file ./9407_GC_C_TIFF_MONTAGES/Ch1_CP0001.tif…
Index in position 2 exceeds array bounds (must not exceed 6).
Error in cif_image_tiling>scale (line 135)
sample = double(reshape(image_raw(1:10,1:10),100,1));
Error in cif_image_tiling>make_montages (line 83)
Ch_IM = scale(get_image(reader, total_cell_count, channel_number), image_size);
Error in cif_image_tiling (line 57)
make_montages(reader, number_of_cells, number_of_channels, image_size, grid_size, output_dir);

I’ve found that changing the number of cells within the gated population exported will fix the issue in most cases, but not all. Any help would be appreciated. Thanks.


#2

Hi,

May I ask how big are the .CIF files in these 3/10 samples? If those are very large .CIF that contain more than 190,000 cells, you may need to break the big population into smaller groups.
This cap (exactly 190,662 cell) seems to be a bug in IDEAS 6.0 export function.


We also have a python stitching script, here, which is an alternative to this MATLAB tiling script. Can you give it a try?

Hope that helps.
Minh


#3

Thanks for the quick reply! The .CIF files I’m trying to tile only contain approximately 5,000 cells each.

Unfortunately I have zero experience with python and very little knowledge of MATLAB or coding in general. I’m good at using FIJI and other image analysis software and can handle writing/editing small macros though. I’m probably pretty close to the prime end user you envisioned would be trying to implement this method into my research.

I’ll see if I can find someone to help me figure out how to get the python stitching script to run.