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I am trying to use the Iterative Deep Learning Workflow on a Windows 10 operating system utilizing a Bash Shell with an Ubuntu command window (Windows Subsystem for Linux) (version 1).
I have followed the aics-ml-segmentation / READ.md instructions exactly. At the install Pytorch setting I chose Stable (1.9.0), Linux, Conda, Python, CPU. I cloned everything and I tried to use the curator_sorting help feature. The first error code I received was module not found error: no module named ‘aicssegmentation’.
I then pip installed aicssegmentation. I tried to use the curator_sorting help function again and received this error.
I can get the Classic Image Segmentation Workflow to work properly on Windows Subsystem for Linux, In addition, we can install the Iterative Deep Learning Workflow on a Mac and can run the curator_sorting help function without an error. However, we can cannot we get the above error on the Ubuntu command window (Windows Subsystem for Linux).
Additional information you might need:
pip show aicssegmentation
pip show aicsmlsegment
Please advise me on what I might be missing or need to install to make the mlsegmenter environment work.
Hello Jianxu_Chen, I want to thank you for your previous post on how to resolve our TKAgg error. Your suggestion worked very well.
I am posting again as I am unable to get the interface to pop up showing specified slices and a max projection within the curator_sorting. I have included screen shots of the images from Fiji that I am using and a screen shot of the Anaconda prompt for Windows. When I press enter this is what happens in the highlighted red rectangle.
Hello @jianxu_chen, I want to thank you for your previous post on how to resolve our TKAgg error. Your suggestion worked very well.
I am reposting a previous question as I am wondering if it might not have alerted you to the post.
I am unable to get the interface to pop up showing specified slices and a max projection within the curator_sorting. I have included screen shots of the images from Fiji that I am using and a screen shot of the Anaconda prompt for Windows. When I press enter this is what happens in the highlighted red rectangle.
hi @RexH , May I ask what will you see in the curator_sorting_record.csv? Also, can you double check the raw .tiff files exist under the directory you used for --raw_path?
I have changed all the files to all be .tif as the batch_processing from the classic segmenter creates .tiff files. Now when I run the curator_sorting I receive these error codes.
Hi @RexH , So sorry if my previous message was confusing. To be clear
DO not change the segmentation files. .tiff is correct
When you type in the command, one of the things you type in is --data_type, currently, your command has --data_type .tiff. Since you raw images are .tif, you need to do --data_type .tif
