angelolab / ark-analysis / 7545
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OME-TIFF Read / Write (#819)

* added OME-TIFF support

* requirements update

* requirement went missing?

* Added tmi to requirements

* set pillow requirement

* update numpy

* add xmltodict to docs

* added tmi to docs/conf.py

* added utility notebook

* switched lambda/map for list comprehension

* switched lambda/map for list comprehension in test function

* Rename `_feature_0` to `_whole_cell` and `_feature_1` to `_nuclear` (#786)

* Initial commit of replacing _feature_0 with _whole_cell and _feature_1 with _nuclear

* Make sure dataset tests include _whole_cell and _nuclear

* Update distance matrix column to be dist_whole_cell

* Patch up marker quantification loading

* Ensure channels for stitch_images test are being passed in correctly

* Rename segmentation label saving to _whole_cell and _nuclear

* Define both the whole cell and nuclear suffix renaming choices for create_deepcell_output

* Change revision to match current PR on HuggingFace with new suffix names

* Patch up calc_dist_matrix suffix

* PYCODESTYLE in data_utils.py

* Patch up deepcell_utils

* Use new HuggingFace commit hash without hidden old files

* Change legacy example_dataset extensions to _whole_cell.tiff

* Make sure neighborhood mask uses _whole_cell.tiff

* Update comment to _whole_cell.tiff too

* Aesthetics

* Patch _feature_0 to _whole_cell to pass neighborhood mask generation test

* Change suffix in the README

* Refer to main branch for HuggingFace

* updated ome-tiff notebook

renamed utility notebook

* undid strange merge

* undid strange merge

* added support for OME-TIFFs with images of multiple resolutions

* added support for OME-TIFFs with images of multiple resolutions

* renamed conversion notebook

* removed unused imports

* fixed channel extraction if a channel has no name

* added example ome_tiff to the Example Dataset

* added example dataset blurb

* up... (continued)

2990 of 3149 relevant lines covered (94.95%)

0.95 hits per line

Jobs
ID Job ID Ran Files Coverage
1 7545.1 (MPLBACKEND=Agg) 34
94.95
 Travis Job 7545.1
Source Files on build 7545