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

Batch Processing does not work for large images (500mB-1GB) #1933

Closed
mayaucsf opened this issue Jan 12, 2019 · 2 comments
Closed

Batch Processing does not work for large images (500mB-1GB) #1933

mayaucsf opened this issue Jan 12, 2019 · 2 comments

Comments

@mayaucsf
Copy link

I have been attempting to process large images in ilastik (500mB - 1GB) but ilastik stops responding whenever I try to batch process even a single image. When I attempted to run object predictions through headless mode, code started opening files and then appeared to stop (no error message) without generating an output file. When I attempted using the batch processing window, the status bar would never move past 0% and ilastik would stop responding and eventually crash. However, when I segmented the same images into 10 tiles (~50mb each), I was able to run all 10 tiles at the same time.

Is there any way to run larger images through the program without the need to segment them?

@constantinpape
Copy link
Member

Which image format are you using?
The best way to process larger images or volumes would be to load them as HDF5 and set an appropriate chunk size.
Ilastik has a data-conversion workflow that should enable you to copy your input data to HDF5.

@k-dominik
Copy link
Contributor

closing with @constantinpape's sound advice

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

No branches or pull requests

3 participants