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

CZI: use alternate source for well identifiers when available #4145

Merged
merged 1 commit into from
Jan 31, 2024

Conversation

melissalinkert
Copy link
Member

Backported from a private PR. This fixes Image/Well mapping for "meander" acquisitions.

Several of our existing test plates are affected, see the forthcoming configuration PR which includes video of the affected data in ZEN. Without this PR, showinf -nopix -omexml on the affected plates should show that each row of wells starts at the left-most (smallest index) column and proceeds to the right-most (largest index) column. With this PR, the same command should show that rows alternate between left-to-right and right-to-left column indexing. The order of rows is unaffected.

This is a really subtle problem and not obvious from visually inspecting the images or even a cursory look at ZEN. Even a basic stitching workflow wouldn't necessarily have picked this up. It's really only obvious when carefully scrolling through each image in ZEN, so reviewing the videos in the configuration PR is important.

Importantly, well metadata can exist in multiple places in CZI datasets, and appears to not necessarily be consistent. That might reflect the physical plate vs the actual acquisition, and can be seen by looking at the original metadata (look for names like A1 and IDs like 1-1).

Added to 7.2.0 for a first look, but since this is a later addition I'm OK with it being bumped to the next milestone if needed.

This fixes Image -> Well mapping for "meander" acquisitions.
@melissalinkert melissalinkert added this to the 7.2.0 milestone Jan 23, 2024
Copy link
Member

@sbesson sbesson left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Tested against a few of the sample CZI plates modified by this change. Without this change, the well-order always start from the left-most colum of each row. With this change included, the order follows a meander-style acquisition strategy. The new order is consistent with the original metadata particular the Information|Image|S|Scene|Name as well as the Information|Image|S|Scene|Shape|{ColumnIndex/RowIndex} values as well as the inspection of theses plates in ZEN while scrolling through the scenes.

The nightly CI builds have been successful with the associated configuration changes which only modify the UnflattenedName, WellColumn keys. Given that #4141 which is already integrated and scheduled for the 7.2.0 release also fixes some image names for the CZI format, I think including this change in the minor release makes sense so that all the known image naming issues are addressed at once.

Copy link
Member

@dgault dgault left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Tested the sample files which have been affected in the config PR and compared to the videos showing the inspection in Zen. Based on the video comparison the updated column indexes appear to be correct.

@dgault dgault merged commit 8570f33 into ome:develop Jan 31, 2024
17 checks passed
@melissalinkert melissalinkert deleted the czi-well-order-develop branch September 6, 2024 19:00
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants