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Align tasks to server/client infrastructure v1.x
No due date•1/1 issues closed- ROI creation from label images - Support overlapping objects
Due by March 31, 2023•6/6 issues closedCover input modality (2) from here: https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/11 Grid imaged with overlap, to be stitched and processed as a single array for the well (with arbitrary ROIs in that well)
Due by December 7, 2022•3/3 issues closedEnable parsing of Yokogawa multiplexed data into the OME-Zarr format
Due by December 16, 2022•6/6 issues closedEnable image analysis & feature measurement workflows that pass intermediates in memory instead of needing to write to disk. To achieve this, we will write a general wrapper for napari workflows.
Due by October 31, 2022•19/20 issues closedWe want to have complete workflows from Yokogawa image data to OME-Zarr, preprocessing, segmentation & feature measurements running for multiple test sets. This should include: Grid-based acquisitions of 3D cell layers (e.g. Cardiomyocytes, to cell segmentation & measurements) Search-first based acquisitions of organoids (to organoid segmentation & measurements and to cell segmentation & measurements) Search-first based acquisition of zebrafish (until single cell segmentation & measurements) The goal is not to reproduce all possible preprocessing, segmentation & feature measurement modalities, but to have basic operations of each type run on different datasets.
Due by September 9, 2022•3/3 issues closedTo enable processing by field of view or arbitrary region, we need to have ROI definitions and the tasks need to be able to parse ROIs, run per ROI and save data per ROI.
Due by September 14, 2022•13/13 issues closedBuild parsing & processing support for non-overlapping search-first data from the Yokogawa
Due by September 21, 2022•4/4 issues closed