CZI reader IlluminationType mapping and ExposureTime units

Hi @dgault,

Two small issues:

  1. When Bio-Formats reads CZI files where the IlluminationType is encoded as “Fluorescence”, it reports:
Unknown IlluminationType value 'Fluorescence' will be stored as "Other"

Could that automatically be mapped to the OME-XML accepted term “Epifluorescence” in the CZI reader to avoid the warning message and make the metadata more complete/correct?

  1. ExposureTime per channel/plane is correctly extracted from the CZI file but the units are frequently incorrect. E.g. all exposure times from CZI files from the Axioscan.Z1 are reported in seconds rather than the correct milliseconds. Looking at the in-CZI metadata I cannot find where they define the exposure time units so maybe they always assume milliseconds?

Thanks,
Damir

1 Like

Hi Damir,

The first one we can certainly resolve, I will open a PR later today to fix the IlluminationType.

For the second point on exposure time, would you be able to provide a sample file which uses milliseconds (can be uploaded to https://www.openmicroscopy.org/qa2/qa/upload/) so we can compare with the other samples we have so we can versify how its stored in the file.

Hi David,
Thanks for the quick reply. I uploaded a 2-channel czi file which shows the ExposureTime units issue. It also shows the “Fluorescence/Other” issue when you run showinf on it. The latter issue may be because the IlluminationType is derived from:
DisplaySetting|Channel|IlluminationType: Fluorescence

rather than:
Information|Image|Channel|IlluminationType #1: Epifluorescence
Information|Image|Channel|IlluminationType #2: Epifluorescence

I didn’t get a confirmation from the QA system but I hope you can find the file.

PS. it may be time to replace the QA system’s uploader. Flash is very old school and not supported by many browsers.

Cheers,
Damir

Thanks Damir, we recived the sample file just fine. I have initially opened a PR to fix the IlluminationType issue in https://github.com/ome/bioformats/pull/3559

For the timing problem I have currently opened a GitHub Issue (https://github.com/ome/bioformats/issues/3560) but I should also be able to provide a PR to fix this shortly.

Hi David,
That’s all great and I look forward to seeing it in an upcoming BF release. Great that you found the DefaultUnitFormat property for time-related info. I had missed that. It does indeed appear in czi files from a couple of different Zeiss instruments we use such as the Axioscan.Z1 and an AxioObserver (w/ ZEN Blue). However, I checked a czi from a Lightsheet.Z1 and unfortunately it doesn’t put in anything similar. I’ll be happy to provide additional example files if that helps.
Cheers,
Damir

As a follow up, the second PR to parse the time units is now open at https://github.com/ome/bioformats/pull/3563