search

mehta-lab / waveorder

Wave optical models and inverse algorithms for label-agnostic imaging of density & orientation.
BSD 3-Clause "New" or "Revised" License
12 stars 3 forks source link

Added example for multiple input deconvolution #96

Closed Soorya19Pradeep closed 1 year ago

Soorya19Pradeep commented 1 year ago

Example script for deconvolution of multiple ometiff inputs to write single zarr output. The example performs phase reconstruction from BF and deconvolution of two fluorescence channels.

talonchandler commented 1 year ago

Thanks @Soorya19Pradeep.

For additional context, this "multiset input" reconstruction takes positions from multiple MDAs (multiple folders each with multiple .ome.tifs) and outputs a single .zarr reconstruction.

@ziw-liu do you think it's best to support "multiset" i/o on the iohub side? I'm leaning towards "yes" since Soorya mentioned that she and her collaborators commonly work in this mode of operation---splitting up a large number of positions into a smaller number of MDAs. If you agree, then you can use the i/o in this script as inspiration, and I think it's best not to merge this here.

Alternatively, we can merge this for now and leave iohub handling until later. I don't this needs to block an initial release of iohub.

ziw-liu commented 1 year ago

support "multiset" i/o on the iohub side

This is definitely a valid feature request. The OpenCell team also generates multiple-MDA (OME-Tiff) datasets.

talonchandler commented 1 year ago

Okay great thanks @ziw-liu! I'll close this for now, and I've opened an iohub issue.

@Soorya19Pradeep thanks a bunch for sharing this script. If you need support with this type of io while iohub is spinning up...let us know.