fractal-analytics-platform/fractal-tasks-core

Issues

• Issue after MIP: Images shown empty in napari

  #735 opened 3 months ago by jluethi
  2

• Better support for OME-Zarr with singleton T dimension

  #663 opened 5 months ago by BioinfoTongLI
  9

• Update setup-python to v5 in all GitHub actions #1192

  #647 opened 3 months ago by tcompa
  0

• Add test that validates NGFF metadata after copy-ome-zarr

  #694 opened 3 months ago by tcompa
  2

• Update README

  #729 opened 3 months ago by jluethi
  0

• Illumination Correction with Channel parallelisation

  #687 opened 4 months ago by jluethi
  0

• Fix import-ome-zarr `types` extraction, when no ROI tables are created

  #701 opened 3 months ago by tcompa
  0

• Review new-image attributes generated by import-ome-zarr

  #700 opened 3 months ago by tcompa
  0

• Add tests for converting 2D data

  #684 opened 3 months ago by jluethi
  0

• Illumination Correction task with `overwrite_input=False` is missing ROI tables

  #723 opened 3 months ago by jluethi
  1

• Centralize copying of tables functionality

  #725 opened 3 months ago by jluethi
  0

• Role of `overwrite` in `cellvoyager_to_ome_zarr_compute.py`

  #720 opened 3 months ago by tcompa
  2

• To define: is `reference_cycle` the right argument name?

  #716 opened 3 months ago by tcompa
  2

• Drop image list updates with only updated_images_urls

  #721 opened 3 months ago by jluethi
  0

• Task output API

  #679 opened 3 months ago by tcompa
  6

• Does dual overwrite parameter in init task & compute task make sense?

  #699 opened 3 months ago by jluethi
  1

• Ensure tasks that add images to a well update well metadata

  #675 opened 3 months ago by jluethi
  2

• Fix how reference cycle is determined in registration tasks

  #707 opened 3 months ago by jluethi
  5

• Add `filelock` to dependencies

  #712 opened 3 months ago by tcompa
  0

• Debug/fix filelock test on macos

  #713 opened 3 months ago by tcompa
  2

• Illumination correction testing: Also test overwrite=False

  #685 opened 3 months ago by jluethi
  0

• Fix illumination_correction without overwrite

  #703 opened 3 months ago by jluethi
  1

• `plate_ones.zarr` test data is missing plate & well metadata

  #708 opened 3 months ago by jluethi
  0

• Review NGFF models & Fractal OME-Zarr models

  #681 opened 4 months ago by tcompa
  4

• Review whether `zarr_url`s have trailing slash or not

  #677 opened 4 months ago by jluethi
  8

• Write version in plate attributes

  #676 opened 3 months ago by jluethi
  3

• Update parameter names in Illumination Correction Task

  #697 opened 3 months ago by jluethi
  0

• Check Task name consistency

  #698 opened 3 months ago by jluethi
  0

• Enable other packages reusing tasks from fractal-tasks-core compound tasks

  #704 opened 3 months ago by jluethi
  3

• Revert local version changes, and make a `1.0.0a0` prerelease

  #690 opened 4 months ago by tcompa
  1

• `zenodo_images_multiplex_shifted` fixture fails with Pillow error

  #674 opened 4 months ago by tcompa
  1

• Update testing helper functions

  #686 opened 4 months ago by jluethi
  0

• Order of task arguments in the schema

  #691 opened 4 months ago by jluethi
  1

• Update tasks to support Fractal V2

  #669 opened 4 months ago by jluethi
  1

• Re-enable manifest validation test

  #682 opened 4 months ago by tcompa
  0

• In `calculate_registration_image_based`, should we check that `zarr_url != reference_zarr_url`?

  #695 opened 4 months ago by tcompa
  1

• Add unit tests for `fractal_tasks_core/tasks/copy_ome_zarr_hcs_plate.py` helper functions

  #696 opened 4 months ago by tcompa
  0

• Add unit test for `create_well_acquisition_dict`

  #693 opened 4 months ago by tcompa
  0

• Add unit test for `get_tables_list_v1`

  #692 opened 4 months ago by tcompa
  0

• Test the multi-plate case of `create_cellvoyager_ome_zarr_init`

  #688 opened 4 months ago by jluethi
  1

• Improve handling of potential existing zarr files in apply_registration_to_image

  #683 opened 4 months ago by jluethi
  0

• In component refactor, ensure consistency about trailing slashes

  #652 opened 4 months ago by jluethi
  1

• Consider including `OMEZarrImage` class in fractal-tasks-core

  #678 opened 4 months ago by jluethi
  1

• Decide on name for zarr path / location identifier & unify use across the repo

  #670 opened 4 months ago by jluethi
  1

• Masking ROI tables should use the labels as index of the table as well

  #672 opened 4 months ago by jluethi
  0

• tables create by `import_ome_zarr` cannot be loaded by `illumination_correction`

  #662 opened 5 months ago by BioinfoTongLI
  3

• Drop assumption that Zarr HCS plates will contain .zarr in their filename

  #660 opened 5 months ago by jluethi
  0

• Expose additional cellpose options in the task

  #649 opened 5 months ago by jluethi
  2

• Manage Cellpose 3.0 transition

  #655 opened 5 months ago by jluethi
  2

• Review how-to-release docs page

  #651 opened 6 months ago by tcompa
  0