Error while saving output file using stardist-predict2d.py

[migueLib]

Describe the bug
I'm using stardist's entry point script stardist-predict2d, the script seems to run until the point of saving the output file..
Raising the following error TypeError: imwrite() got an unexpected keyword argument 'compress'

I don't think there's a 'compress' argument on imwrite()

To reproduce
I'm using some ome.tif files to segment.
And running it from the command line using the following command

stardist-predict2d -i ~/data/plate_2024_01_29_A3_nuclear/ometif/Plate_2024_01_29_A3_s01c1.ome.tif -o ~/data/plate_2024_01_29_A3_nuclear/segmentation/stardist/ -m 2D_versatile_fluo -v
Expected behavior
I would have expected it to run and output the file on the specified directory

Data and screenshots

Environment (please complete the following information):

• StarDist version [0.9.1]
• CSBDeep version [0.8.0]
• TensorFlow version [2.15.0]
• OS: [Mac]
• GPU memory (if applicable): [ 32 GB M1 mac]

You may run this code and paste the output:
stardist: 0.9.1
csbdeep: 0.8.0
tensorflow: 2.15.0

WARNING:tensorflow:From :2: is_gpu_available (from tensorflow.python.framework.test_util) is deprecated and will be removed in a future version.
Instructions for updating:
Use tf.config.list_physical_devices('GPU') instead.
tensorflow GPU: False

[uschmidt83]

Hi @migueLib, thanks for raising this issue.

I don't think there's a 'compress' argument on imwrite()

There was until version 2022.4.22 of tifffile (see changelog).

I just replaced the use of compress in one of our example notebooks, but I overlooked the prediction scripts. We will fix this for the next release.

In the meantime, you can try downgrading tifffile to an earlier version, e.g. pip install "tifffile<2022.4.22".
(Beware that this can potentially break another package in your environment.)

[migueLib]

@uschmidt83 Thanks a lot for the quick reply!

Is there any plan of joining --outdir and --outname flags into one?