stardist / stardist

StarDist - Object Detection with Star-convex Shapes

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Running stardist inside imagej, there is a problem importing the trained model

baiye1100 opened this issue · comments

Describe the bug
Models trained with tensorflow2.X do not work properly with fiji. fiji uses tensorflow1.15 by default, and models that want to train with tensorflow2.X need to switch to version 1.14 in Fiji, but have been failing
To reproduce
Steps to reproduce the behavior, ideally by providing a code snippet, Python script, or Jupyter notebook.

Expected behavior
A clear and concise description of what you expected to happen.

Data and screenshots
If applicable, add data (e.g. images) or screenshots to help explain your problem.

Environment (please complete the following information):

  • StarDist version [e.g. 0.6.2]
  • CSBDeep version [e.g. 0.6.1]
  • TensorFlow version [e.g. 2.3.1]
  • OS: [Windows, Linux, Mac]
  • GPU memory (if applicable): [e.g. 8 GB]

You may run this code and paste the output:

import importlib, platform

print(f'os: {platform.platform()}')
for m in ('stardist','csbdeep','tensorflow'):
    try:
        print(f'{m}: {importlib.import_module(m).__version__}')
    except ModuleNotFoundError:
        print(f'{m}: not installed')

import tensorflow as tf
try:
    print(f'tensorflow GPU: {tf.test.is_gpu_available()}')
except:
    print(f'tensorflow GPU: {tf.config.list_physical_devices("GPU")}')