Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

QuPath doesn't support some channel combinations through Bio-Formats #956

Closed
petebankhead opened this issue Apr 23, 2022 · 0 comments · Fixed by #958
Closed

QuPath doesn't support some channel combinations through Bio-Formats #956

petebankhead opened this issue Apr 23, 2022 · 0 comments · Fixed by #958
Labels
Milestone

Comments

@petebankhead
Copy link
Member

Bug report

Describe the bug
Bio-Formats can support more ways of handling channels than QuPath can currently read.
Specifically, this includes multiple channels with multiple samples-per-pixel in each channel.

The effective number of channels comes from adding all the samples across all the channels.

This problem turned up with a polarised light scan in CZI format: https://forum.image.sc/t/qupath-cant-open-polarized-light-scans/65951

To Reproduce
Awkward... Can likely only be reproduced using an image where

metadata.getChannelCount(series) < nChannels

and where the extra channels can be accessed via metadata.getChannelSamplesPerPixel(series, channelInd).

Expected behavior
QuPath properly opens all channel combinations supported by Bio-Formats.

Desktop (please complete the following information):

  • OS: All
  • QuPath Version v0.3.2 and all previous

Additional context
When this occurs, we could have mixed modes... like brightfield & something else. So a satisfying fix might require supporting multi-modal images.

@petebankhead petebankhead added this to the v0.4.0 milestone Apr 23, 2022
petebankhead added a commit to petebankhead/qupath that referenced this issue Apr 23, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant