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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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LIF: Improve handling of tiles and stitching / incorrect and skewed tiles #3836

Open dgault opened 2 years ago

dgault commented 2 years ago

Issue was raised on forum thread https://forum.image.sc/t/could-bio-formats-interpretation-of-lif-files-containing-tiles-and-stitched-images-be-improved/64216

Bio-Formats currently opens every tile as a seperate series, so using an example from the thread, a file containing 3 stitched images of 150 tiles will currently open as 450 series in Bio-Formats (most recently tested with 6.10.0). A current work around for this for users is to used Read My LIFs or split the acquisitions into different projects using LAS X

A sample file was provided in thread (https://zenodo.org/record/6606445#.Yp4MDfPMI_U) which displays the issues when multiple image types are found in the same file. From the description of the sample file:

This is a lif-file with two simple multichannel z-stacks. Then further multichannel z-stacks follow which are part of stitched merge image which is the last image in the file. This larger merged image is not read correctly by bioformats (v6.9.1). If the 2 z stacks not belonging to the merged image are deleted from the lif file or moved behind the merged image using the Leica LASX software, bioformats displays the merged image correctly.

imagesc-bot commented 2 years ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/could-bio-formats-interpretation-of-lif-files-containing-tiles-and-stitched-images-be-improved/64216/11

imagesc-bot commented 2 years ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/feature-request-easier-image-selection-from-lif-files/68989/7

dgault commented 1 year ago

A further issue has been raised on forum thread https://forum.image.sc/t/some-images-within-a-lif-file-become-garbled/76807/2

In this case the file contains a combination of tiles as individual series and merged images also as separate series. A number of tiles appear to be skewed as if the dimensions are incorrect and the stitched images look as though the wrong tiles are being read. Screenshots of this behaviour are available on the thread and can be recreated with the sample file on Bio-Formats 6.11.1

The user reported that separating the original file into individual lif files allowed the files to be read correctly.

A sample file was provided on the thread and will shortly be available on inbox/imagesc-76807

imagesc-bot commented 1 year ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/some-images-within-a-lif-file-become-garbled/76807/3