Closed vzickus closed 6 years ago
Following the filenames in the tutorial and the accompanying resource file, I had used the wrong annotation file.
vzickus - I'm running into the same issues: this and #6. Im using the annotation_25_full_color.tif that came with the download from OSF website. Which is the correct annotation file? ta!
This has been quite some time ago, and now I cannot remember (for the benefit of others, that last comment should have been more descriptive to be honest). If I don't forget, I will try to have a look tomorrow.
Alright, thanks!
OK, so in my parameter_file scripts I have:
AtlasFile = os.path.join(PathReg, '2p_mouse_brain_data_25um.tif');
AnnotationFile = os.path.join(PathReg, 'annotation_25_full.nrrd');
Where PathReg is just </path/to/atlas/files>
So .nrrd must be the correct annotation file to use. Can you try and let me know if this works?
Seemed to have worked - thanks, much appreciated
I think I am having issues caused by this bit of code in the process_template.py script.
The first red flag is that the terminal outputs "Processed 0/6059", but never increases and the script ends without any error. However, the output of "Annotated_counts.csv" and "Annotated_counts_intensities.csv" only contain one row with three columns. I ran the "Check Cell detection" bit of the code, and can clearly see a lot more cells detected. Any ideas what could be the cause of this? I initially ran into issue #6, but after hard-coding the correct path, I am still getting only a single row input in the aforementioned files.