Sébastien Besson

Java 17 support

8

Fixes #3659 Java 17 LTS was released in September 2021 and in getting increasing used in the community by consumers of Bio-Formats e.g. `bioformats2raw` or `QuPath`. While there has been...

OME-TIFF reader: getCanonicalPath causes containment regression in OMERO context

1

See https://forum.image.sc/t/no-access-to-some-images-in-omero-securityviolation-metadata-companion-ome-accesses-data-outside-managed-repository/69453 The issue can be reproduced either using the public sample shared in the image.sc thread of any companion fileset like the official OME-TIFF sample athttps://downloads.openmicroscopy.org/images/OME-TIFF/2016-06/companion/. The source of...

https://forum.image.sc/t/bioformat-upgrade-matlab/26099 revealed a few issues with the `UpgradeChecker` installation logic affecting callers like `bfUpgradeCheck`. The most prominent issue is that the CI logic within the class is no longer functional....

Add support for multi-Z images exported from Perkin Elmer Columbus

1

See https://forum.image.sc/t/bio-formats-doesnt-open-columbus-xml-file-properly-with-z-stack/43659 and https://forum.image.sc/t/import-of-old-operetta-images-bioformats-incompatibility/64139 A new format reader for the export data generated by PerkinElmer Columbus systems was introduced in https://github.com/ome/bioformats/pull/2830 and released since Bio-Formats 5.5.0. This implementation reader was...

SVS: handle optional label and macro images

4

See https://forum.image.sc/t/correct-way-to-convert-svs-slides-for-omero-import/50942/. As described in the `Digital Slides and Third-Party Data Interchange`, a SVS file may contain a label and/or a macro image. In the majority of the samples, these...

MRCReader: invert planes in Y for FEI variants

2

See https://forum.image.sc/t/bio-formats-does-not-read-tiff-mrc-pixel-size-from-drag-and-drop/53695 More specifically, from https://bio3d.colorado.edu/imod/doc/mrc_format.txt ``` IMOD will always write files in this orientation but will recognize files with an inversion in Y (first row of pixels as the...

Citation file format and record versioning

5

Firefox: OS X 11.6.1 ## Describe the bug Zenodo has recently announced the support for the CFF file format in its GitHub integration (https://twitter.com/zenodo_org/status/1420357001490706442). This integration raises a couple of...

Disallow mismatching axes units and types

3

See discussion at https://github.com/ome/ngff/pull/87#discussion_r797433723 Units were introduced in https://github.com/ome/ngff/pull/57 at a SHOULD level of requirement, primarily for extensibility reasons as well as support for axes with arbitrary units. A large...

`ome-zarr-py 0.3.0`includes support for reading/writing datasets compliant with the [OME-NGFF 0.4 specification](ngff.openmicroscopy.org/0.4/) #162 in particular introduced support for writing the `coordinateTransformations` metadata such as the mandatory `scale` at the `multiscales.datasets`...

Deprecate chunks keyword in write_image` and write_image_multiscales

2

See conversation at https://github.com/ome/ome-zarr-py/pull/161#discussion_r800575583 The `storage_options` keyword introduced in 0.3.0 should support setting the `chunks` to the Zarr dataset. This option also gives the extra flexibility of being able to...