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fishlineautomation's Introduction

FishlineAutomation - Pipeline for automating the processing and registration of gene lines in zebrafishes.

Script and notebook to perform pre-processing and preparing zebrafish image files of project from Baier Lab.

To install the respective libraries: a. Install Conda b. Create conda environment and install the following libraries using "conda env create --file environment.yml"

fishlineautomation's People

Contributors

keshavprasadgubbi avatar joe311 avatar

Watchers

James Cloos avatar avatar

fishlineautomation's Issues

Saving the czi split channel files as tiff files not working

This error occurs intermittently, some time occurring for the same file and sometimes not, with all other factors being unchanged. Related to line 45 in czi.py.

_```
Traceback (most recent call last):
File "C:/Users/keshavgubbi/Desktop/ATLAS/S1/czi.py", line 45, in
with tiff.TiffWriter(os.path.join(c_path, f'{name}_ch{ch_num}.tif')) as tifw:
File "C:\Users\keshavgubbi\Anaconda3\lib\site-packages\tifffile\tifffile.py", line 1129, in init
self._fh = FileHandle(file, mode='wb', size=0)
File "C:\Users\keshavgubbi\Anaconda3\lib\site-packages\tifffile\tifffile.py", line 8831, in init
self.open()
File "C:\Users\keshavgubbi\Anaconda3\lib\site-packages\tifffile\tifffile.py", line 8844, in open
self._fh = open(self._file, self._mode)
OSError: [Errno 22] Invalid argument: 'C:\Users\keshavgubbi\Desktop\ATLAS\S1\data\czidata\2_ch0.tif'

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