angelolab / ark-analysis / 6164

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Example Dataset (#685)

* added datasets as requirement

* added dataset download function

* doc test fix

* Notebook 1 updated for example dataset

* Remove call to is_mibitiff cell in testbook script

* removed data/* and added data/ to the .gitignore

* Remove .DS_Store, change input_dir variable back to tiff_dir (more intuitive), and update notebook tests

* Remove MIBItiff test

* Change input_dir to tiff_dir

* Nuke another instance of input_dir

* added original dataset back in so tests can pass

* updated nb1 and nb2 to use segmentation/

* nb3 paths fixed

* reverted pixie subdir for nb2,3

* Change testbook path to reflect new directory structure

* Remove unneeded cell outputs

* LDA path updates

* remove test import

* Prevent division by NA if a column is all 0

* `cell_size` of 0 fixed, deepcell_service_utils::_convert_deepcell_seg_masks, change dtype from int16 to int32

* deepcell bytes conversion fix + test

* seaborn fix

* removed changes for nb2, nb3, nb4

* removed changes for LDA, example neighborhood analysis, visualization notebooks

* revert pixel clustering test

* testbook fix

* testbook fix

* dataset download test

* reverted pytest-randomly

* made requested changes

* download dataset function, will save to default cache location, and copy data over to ark-analysis/data

* test fix

* fixed paths

* nb1 fix

Co-authored-by: alex-l-kong <alkong@ucdavis.edu>
Co-authored-by: csowers <camisowers@g.ucla.edu>

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