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Add reader for Ventana .bif files #3336
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Ventana .bif files are TIFF files where the first two IFDs correspond to label/overview/macro images and the remaining IFDs form a pyramid. Each IFD in the pyramid stores the image as tiles that are typically at least 1k x 1k.
Not all stored tiles are used; the largest IFD in the pyramid contains XML that defines one or more
In the largest pyramid resolution, each TIFF tile corresponds to one acquired tile. In smaller resolutions, each TIFF tile is n x n acquired tiles with overlaps embedded. To read smaller resolutions, each TIFF tile must be split apart and reassembled using the absolute positions that were calculated for the largest resolution.
Ventana .tif files are similar to .bif files, but have been processed to remove all overlaps and all scanned area metadata. The IFD ordering and magnification metadata is the same as in .bif, but the tiles can be treated as normal TIFF tiles.
To my knowledge, there is no freely available software that can be used to get a ground truth, so this is a little difficult to thoroughly validate. Comparing the pyramid images to the label/thumbnail image is probably the most reliable check. The pyramid images can also be checked for any really obvious seams between tiles that indicate incorrect overlap calculation.
There is also a
This will require a minor release but isn't critical for 6.1.0, so feel free to exclude in favor of other readers.
See https://web-proxy.openmicroscopy.org/east-ci/job/BIOFORMATS-test-folder/61459/console, the reader seems to misdetect TIFF files that should be detected as Metamorph.