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ome / bioformats

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
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Added support for ColumbusReader to import data with z stacks #4147

Closed TBlackmore closed 2 months ago

TBlackmore commented 5 months ago

Following up on issue #3791 I had the same problem importing data exported from PerkinElmer (Revvity) Columbus into Omero. No Z stacks were coming through. I've ammended the ColumbusReader and run some tests. I have some test data I can provide, but I'm having an issue getting into Zenodo at the moment.

dgault commented 5 months ago

Thanks @TBlackmore for opening the PR, if are able to provide some sample files that would greatly help the testing.

Also, we have a Contributor License Agreement for the project, would you be able to sign and return the form following the instructions on https://ome-contributing.readthedocs.io/en/latest/cla.html

TBlackmore commented 4 months ago

No worries @dgault :-) Happy to be helping!

I've uploaded a two test datasets here. One with single plane tifs, and one with multiplane.

I've also submitted the license agreement.

Let me know if there's anything else I can do to get this PR done.

dgault commented 4 months ago

Thanks @TBlackmore, having the samples to test with is a great help, we will aim to get this PR reviewed within the next week and let you know if there are any changes or updates required.