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STOmics / SAW

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partially initialized module 'cv2' has no attribute 'gapi_wip_gst_GStreamerPipeline' #96

Closed tenlives closed 4 months ago

tenlives commented 4 months ago
1708650368333

at 'image processing and registration start' step, it raises above error. Is there a soultion? Thank you!

tenlives commented 4 months ago 
/usr/bin/time -v singularity exec ${sif} register \
    -i ${imageTarFile} \
    -c ${iprFile} \
    -v ${outDir}/02.count/${SN}.raw.gef \
    -w True --core ${threads} \
    -o ${outDir}/03.register

When run this step, it raises above error. The SAW version is 7.0.

Clouate commented 4 months ago

This is generally caused by package conflicts in the system environment. I'm sorry that we have less relevant experience and you could try to reconstruct the conda environment.

tenlives commented 4 months ago

This is generally caused by package conflicts in the system environment. I'm sorry that we have less relevant experience and you could try to reconstruct the conda environment.

Thank for your advice! it works for me

tenlives commented 4 months ago
1708693647083

Whether it indicate that the imageRecordFile ipr file is invalid?

Clouate commented 4 months ago

It means the image did not pass QC in ImageStudio, you may need to do manual tissue segmentation in ImageStudio and manual registration in StereoMap, refer to 'Scripts/stereoPipeline_v7.0_manual_part1.sh' and 'Scripts/stereoPipeline_v7.0_manual_part2.sh' .

tenlives commented 4 months ago

It means the image did not pass QC in ImageStudio, you may need to do manual tissue segmentation in ImageStudio and manual registration in StereoMap, refer to 'Scripts/stereoPipeline_v7.0_manual_part1.sh' and 'Scripts/stereoPipeline_v7.0_manual_part2.sh' .

Thank you! It is very helpful.