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

Initialize function performance issues on HCS datasets #124

Closed
DavidStirling opened this issue Jan 15, 2024 · 0 comments · Fixed by #128
Closed

Initialize function performance issues on HCS datasets #124

DavidStirling opened this issue Jan 15, 2024 · 0 comments · Fixed by #128
Assignees

Comments

@DavidStirling
Copy link
Member

DavidStirling commented Jan 15, 2024

Following on from #116, the scanning process appears to be taking an unreasonably long time when working with some HCS datasets.

As an example, the BBBC017 dataset runs through bioformats2raw reasonably quickly to create our source Zarr, but raw2ometiff conversion gets hung up during initialisation. Data is available here, just one of the .zip files (1 plate) is sufficient. This is all running with default arguments.

There are a few thousand series within the input zarr. From a quick look it seems like examining the contents of each series takes ~0.2s each to start, which isn't ideal. However by the time we're at s=2000 they're taking ~2.5 seconds each. Every image in the dataset should be of similar size/format so I can't see an obvious reason to expect this beyond a bug somewhere.

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 a pull request may close this issue.

2 participants