Jupyter notebook motioncorrect_timestamp_errors.ipynb calls motioncorrect_timestamp_errors.py
and replicates the following errors.
These errors occur when multiple plane tiff files are used and fetched to NWB objects.
- ERROR I :
ValueError: 'CorrectedImageStack' already exists in MotionCorrection 'MotionCorrection'
Each session has multiple planes, hence, I would like to store multiple CorrectedImageStacks in the MotionCorrection object. Currently, I’m appending the corrected_image_stack and trying to store it in the MotionCorrection object on here. This is when I receive the following error: ValueError: 'CorrectedImageStack' already exists in MotionCorrection 'MotionCorrection'. It looks like it is not allowing me to save multiple CorrectedImageStack into the MotionCorrection object because when I tried the following it worked: motion_correction = MotionCorrection(corrected_image_stacks=corrected_image_stacks[0])
- ERROR II :
ValueError: RoiResponseSeries.__init__: incorrect shape for 'timestamps' (got '(170, 26100)', expected '(None,)')
Each ROI has a different timestamp, which is why I would like to store timestamps as 2D arrays (hence, the shape becomes : 26100, 170).
To run the notebook:
- Clone the repository
- Run the cells of
motioncorrect_timestamp_errors.ipynb - You will first encounter Error II (i.e. the timestamp issue). This is because the there is no NWB MoitonCorrection object while processing the first plane.
- To bypass the timestamp issue, you can set
timestamp = timestamp[0]here.
The tiff file used has a single plane but the code is setup in a way to replicate the behavior of a multiple plane tiff file processing.
Note: This example is prepared using a different tiff file and using some random dummy data. Hence, it might not match the outputs if Suite2p is run outside.