Bio-formats exposure time incorrect when importing VSI files

I am using bio-formats (version 23 October 2020) to load data in from a VSI file for further processing. When looking at the generated xml metadata the exposure information is incorrect, with all the planes having the same exposure time.


When opening the same file in VS Desktop it shows as expected that the different channels have different exposure times
image

The data shown in the “Original Metadata” window seems to have the correct values
image

It looks like the exposure time from the last channel has been used for all the channels when generating the XML datafile.

Has anyone else experienced this issue? How would I go about getting the correct exposure values in the xml file produced?
Many thanks in advance for your help.

This looks to be a bug in the Bio-Formats reader and I have opened a new GitHub Issue (https://github.com/ome/bioformats/issues/3642). If you have a sample file that we could use to reproduce for testing purposes you can upload it to https://www.openmicroscopy.org/qa2/qa/upload/

As a temporary workaround you should be able to load the values from the original metadata, are you using a macro or script for processing?

Thanks for the response and creating the github issue (which I’m also watching).

I’ve just asked my colleague who’s data I noticed this issue in for permission to share a file with you for debug purposes. I’ll upload an example file when I have permission for it.

I’m using it in a script to automatically generate the metadata xml file (and some tifs) which are then read in by another system.

I’ve just uploaded a VSI file for you. BTW, finding a PC with flash installed was tricky (I ended up using a
VM), this will only get harder when Flash goes end of life in 28 days.

Thanks for uploading the sample file Philip, those test files are a great help in trying to get fixes in place. I can confirm the issue is reproduced with the latest Bio-Formats and have updated the GitHub Issue.