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View Code? Open in Web Editor NEWFiles used to test OME-TIFF images for BIDS-microscopy
License: MIT License
Files used to test OME-TIFF images for BIDS-microscopy
License: MIT License
I tested the notebook on Ubuntu 20.04 in WSL 1:
conda install
from pyvips
(https://libvips.github.io/pyvips/README.html#conda-install). It already includes the libvips
library so I commented those lines in the notebook.matplotlib
, jupyter
and imagecodecs
as well.I have a few questions/observations about the tests.
1) Read OME-TIFF image + metadata:
OME series: failed to read 'tubhiswt_C1.ome.tif'
, which is normal because the file C1
is not in the repo.C1
, ex: {'UUID': {'FileName': 'tubhiswt_C1.ome.tif', 'value': 'urn:uuid:f801ea0a-e93e-4f4f-99b3-7ecc15048c12'}, 'FirstC': 1, 'FirstT': 2, 'FirstZ': 0, 'IFD': 2, 'PlaneCount': 1}
Write OME-TIFF image + metadata:
tifffile
in Fiji/Bioformats
, I get an image and metadata with 30 "timepoints" (SizeT = 30
) and 1 "channel" (SizeC = 1
).compress=7
means in the call of tifffile.imwrite
.3.1) TIFF to OME-TIFF:
pyvids
in Fiji/Bioformats
, I got the right dimension in metadata but the image is a repetition of a tiles?[WARN] SamplesPerPixel mismatch: OME=-1, TIFF=1
[WARN] Image ID 'Image:0': missing plane #0
[WARN] Using TiffReader to determine the number of planes.
3.2.2) Generate the OMETIFF with the NDPI data:
Fiji/Bioformats
, the image on the 3 channels appears totally black, although the validation at point 3.2.3 shows the correct image. I updated the Bioformats version to the latest i.e. 6.6.1.A declarative, efficient, and flexible JavaScript library for building user interfaces.
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