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matjesg / deepflash2

A deep-learning pipeline for segmentation of ambiguous microscopic images.
https://matjesg.github.io/deepflash2/
Apache License 2.0
58 stars 11 forks source link

Groundtruth calculation is broken since update of simpleITK #3

Closed AmSchulte closed 3 years ago

AmSchulte commented 3 years ago

The calculation of the ground truth is broken since the release of simpleITK 2.0

Solution is to add "!pip install SimpleITK==1.2.4" manually to the google colab. Maybe it would be good to add a requirements.txt to the installation and add an upper version bound to the installed dependencies.

matjesg commented 3 years ago

Thanks for bringing up the issue @AmSchulte , i hope it is solved this way!

requirements.txt to the installation and add an upper version bound to the installed dependencies.

SimpleITK is not part of the requirements of deepflash2 anymore. Only the ground truth estimation notebook uses and installs SimpleITK==1.2.4 if required