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Integrating (BioIO: https://github.com/bioio-devs/bioio) to convert to ome-zarr - Update iohub dependencies (zarr, etc.) for compatibility - Migrate to zarr 0.5 Completed acquisitions - Implement FileDialog/filter based on supported files that can be converted/reconstructed - Extract metadata and present/populate field - Reconstruction options: Single time-point, up to current time-point, continuous reconstruction Live acquisitions (supported by BioIO) - You can read ND2 files during a live acquisition by using a Python library called nd2. It provides a fast, pure-Python solution for incrementally reading from files that are still being written by Nikon's NIS-Elements software. Other general-purpose image readers, like Bio-Formats, are not designed for this specific "live-read" purpose. - To read a CZI file while it is still being acquired, you need to use a robust Python library designed for this purpose, such as pylibCZIrw, czifile, or aicsimageio. The key is to open the file in a read-only context that is resilient to file changes. The Zeiss pylibCZIrw library is specifically built to handle this by automatically detecting and invalidating its internal cache when the file is modified. - To read an OME-TIFF file while it is actively being acquired, you need a reader that can handle incomplete or growing files. The standard tifffile Python library can handle this, and if you are using Micro-Manager, the pycromanager library provides a robust solution. Resource allocation - Ensure enough resources computation/memory are available for live acquisition. Limit reconstruction resources if needed.
Overdue by 7 month(s)•Due by September 19, 2025- No due date•9/9 issues closed