CellSeg
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michaellee1
Getting error "ValueError: could not broadcast input array from shape (7973,184) into shape (7973)" Is there any changes in the updated code. Can you please share the latest working code....
Hi, while investigating the mask growing method, I have come across some unexpected behavior, which looks incorrect to me. For example, notice how the mask on the left side of...
Hello, how can I use multiple channels to segment the image? Now I have 24 channels in the CHANNEL_NAMES.txt but it seems the parameter NUCLEAR_CHANNEL_NAME only accpect one single string....
Hi! Thank you for making Cell Seg, this is an awesome tool! I was wondering if there is a way to import the masks into ImageJ and/or QuPath so that...
I have processed CODEX data (that I assume came from the new PhenoCycler-Fusion system) saved as a single qptiff file. This format isn't quite what CellSeg expects for codex. With...
`OSError: Unable to open file (unable to open file: name = '..\CellSeg\src\modelFiles\final_weights.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)` Can...
updated repo using up to date tensorflow (necessary if using GPU) can be found by following instructions of this PR: https://github.com/michaellee1/CellSeg/pull/60
Updated to work with newer versions of TensorFlow and to use it as a headless library.
Found this error when attempting to import packages on ubuntu. A simple solution was to run ``` conda install -c conda-forge gcc=12.1.0 ``` Might just need an update to the...
For some users (eg those using ondemand) it would be useful this: `import sys` `sys.path.append('name of your CellSeg_directory')` This enables it to import all the functions even if jupyter is...
