search

czbiohub-sf / iohub

Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata
https://czbiohub-sf.github.io/iohub/
BSD 3-Clause "New" or "Revised" License
30 stars 7 forks source link

Error reading MM data from DragonFly #240

Closed Soorya19Pradeep closed 1 month ago

Soorya19Pradeep commented 2 months ago

The following error message is seen when I try to convert Micromanager data /hpc/instruments/cm.dragonfly/Dashboard_aim2/2024_08_14_ZIKV_pal17_48h/2024_08_14_ZIKV_pal17_48h_1/ using iohub convert function:

WARNING:tifffile.tifffile:<tifffile.TiffPage 0 @71365> <tifffile.TiffTag 50839 @71547> invalid value offset 0 WARNING:tifffile.tifffile: failed to read display settings: invalid display_header 0 WARNING:tifffile.tifffile:<tifffile.TiffPage 0 @71365> <tifffile.TiffTag 50839 @71547> invalid value offset 0 WARNING:tifffile.tifffile: failed to read display settings: invalid display_header 0 Traceback (most recent call last): File "/hpc/mydata/soorya.pradeep/recOrder/bin/iohub", line 8, in sys.exit(cli()) File "/hpc/mydata/soorya.pradeep/recOrder/lib/python3.10/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/hpc/mydata/soorya.pradeep/recOrder/lib/python3.10/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/hpc/mydata/soorya.pradeep/recOrder/lib/python3.10/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/hpc/mydata/soorya.pradeep/recOrder/lib/python3.10/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/hpc/mydata/soorya.pradeep/recOrder/lib/python3.10/site-packages/click/core.py", line 783, in invoke return __callback(args, kwargs) File "/hpc/mydata/soorya.pradeep/recOrder/lib/python3.10/site-packages/iohub/cli/cli.py", line 119, in convert converter.run(check_image=check_image) File "/hpc/mydata/soorya.pradeep/recOrder/lib/python3.10/site-packages/iohub/convert.py", line 575, in run self._init_zarr_arrays() File "/hpc/mydata/soorya.pradeep/recOrder/lib/python3.10/site-packages/iohub/convert.py", line 428, in _init_zarr_arrays self._init_hcs_arrays(arr_kwargs) File "/hpc/mydata/soorya.pradeep/recOrder/lib/python3.10/site-packages/iohub/convert.py", line 434, in _init_hcs_arrays self._create_zeros_array(row, col, fov, arr_kwargs) File "/hpc/mydata/soorya.pradeep/recOrder/lib/python3.10/site-packages/iohub/convert.py", line 450, in _create_zerosarray = pos.create_zeros(arr_kwargs) File "/hpc/mydata/soorya.pradeep/recOrder/lib/python3.10/site-packages/iohub/ngff.py", line 715, in create_zeros self._check_shape(shape) File "/hpc/mydata/soorya.pradeep/recOrder/lib/python3.10/site-packages/iohub/ngff.py", line 746, in _check_shape raise ValueError(msg) ValueError: Image has 2 channels, while the dataset has 1.

I can open the images using MicroManager.

kfweng0512 commented 2 months ago

I also encountered the same warming message when converting my newly generated dataset from Hummingbird. I can open my dataset by using the micromanager as well.

ziw-liu commented 1 month ago

~@Soorya19Pradeep Is this still an issue? I see that this file has been converted at:~ ~Edit: nvm those are empty zarr stores.~ Edit of edit: I spoke too soon... This plate does look like a successful conversion:

/hpc/projects/intracellular_dashboard/viral-sensor/2024_08_14_ZIKV_pal17_48h/0-convert/2024_08_14_ZIKV_pal17_48h.zarr
ziw-liu commented 1 month ago

Likely due to using an old iohub version without the multicam fixes.