baigouy / tissue_analyzer Goto Github PK

In some instances, the tracking algorithm (dynamic/non-static option) assigns the same track_id to multiple local_ids (i.e. cells).

Hi,
I am trying to use Tissue Analyzer on Mac (OS 13.0).
When I try to open the GUI using the line 'python -m epyseg.ta', I get the following message: 'Illegal instruction: 4'.
Any ideas as to what could be causing this and how to solve it?
Thanks!

Hi, I'm a running into an issue when trying to export data from TA using the 'Export cell data' function on the 'Plots' tab. After I make selections of the data to be output in the first pop-up window 'select and re-order columns', nothing happens and TA / ImageJ freezes (i.e., I get the pinwheel of death and 'application not responding', on Mac OS).

My dataset is relatively small (~200-300 cells, 100 time points), so I don't think it is a memory issue, so I'm wondering if something else could be the source of the problem.

Also, I'm new to using TA, so it's totally possible that I missed a necessary step that has to happen before exporting data. Before trying to export, I segmented cells, did the correction and post-processing, and ran the cell tracking algorithm. Is there anything else that needs to be done before data can be exported?

Last, for reference, my FIJI installation is up-to-date, and I am working with Mac OS 13 with the M1 apple silicon processor.

Thank you!

Hello and thank you very much for this tool!
Although I've been using TA successfully for quite some time now, I am now getting an error when opening my files.
I drop my files on the List, but then when I select an image to work with the BioFormats Import options window pops up. If I just select to continue with default options, nothing happens and I cannot open my files, or if I select to view with "standard ImageJ", then I get the error attached. Any ideas on how to go around this? Would be much appreciated!

Thank you so much in advance!

Hi,

I can vizualize the tracked cells by exporting the tracked_cells_resized.tif from pyTA, but then I'm not sure how to find the corresponding track id in the cells.csv for a given tracked cell in the tracked_cells_resized.tif. Any hint here?

Many thanks!
Son

When I try to install pyTA with the instructions given here, I'm getting this error:
python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [8 lines of output]
Traceback (most recent call last):
File "", line 36, in
File "", line 34, in
File "C:\Users\EMBRG\AppData\Local\Temp\pip-install-k5ny9zhd\sklearn_6b309237fa154cc7bf3f1beff1e70f92\setup.py", line 10, in
LONG_DESCRIPTION = f.read()
File "C:\Users\EMBRG\anaconda3\envs\TA\lib\encodings\cp1252.py", line 23, in decode
return codecs.charmap_decode(input,self.errors,decoding_table)[0]
UnicodeDecodeError: 'charmap' codec can't decode byte 0x8f in position 7: character maps to
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

Could you please look into it? Thanks.

Hello,
I have been using python Tissue Analyzer for Windows to do segmentation of epithelial cells and noticed that whenever I tried to run the advanced segmentation and tracking correction, the window crashes and I am given an "unhandled Python exception." Is there any way around this? Any help would be appreciated.

I am unable to open any image files in tissue analyser plugin. I tried different image formats, also tried reinstalling the plugin. But couldn't get the image file to open. Either there is a severe lag or some other issue I cannot troubleshoot. Can someone help me with this?

When I try to export cell data/ export bond data from the FIJI plugin GUI, I am getting a warning box which says 'Sorry but there seems to be a problem with the DB associated to file', could you please look into this? The plugin was working fine for me last week.

Hello, I'm having a problem installing tissue analyzer on a macbook (os 12.6). I'm not able to create a conda environment with python 2.7, I think due to the issue discussed here: https://stackoverflow.com/questions/67380286/anaconda-channel-for-installing-python-2-7

Is there a way to use a different python version?

Many thanks for the help and the great software!