Cameron Sowers

@alex-l-kong @srivarra Can you guys just take a preliminary look? I'll do a second pass when the notebook tests are running.

If we do this, a neighbors matrix will be generated and saved based on the provided subset of cells, which could potentially cause issues in other spatial scripts. It likely...

@srivarra @alex-l-kong @ngreenwald @jranek Lmk your thoughts. I'm leaning towards a hard switch since we just released v0.7.0 of ark and anyone super committed to staying away from AnnData can...

Looks cool! We can take the existing OME TIFF conversion code and add it into a notebook that also does the AnnData conversion for the cell table.

Just a minor comment on selecting a nested file which should have the same name for all users, so it probably can just be assigned by us rather than making...

Hi @FaehlingT, we have a [line of code](https://github.com/angelolab/ark-analysis/blob/e4caefeb5e1c8f74939efe18b1dd3d8382aec5db/src/ark/utils/plot_utils.py#L725) within the function that handles None input by changing it into an empty string in order to work with `os.path.join()`. It was...

Hi @FaehlingT. That variable name is correct, and was added to the notebook and `create_pixel_matrix()` function in PR #985. Getting a TypeError here means your code is likely out of...

Hi @smith6jt-cop, thanks for catching this outdated readme section! We'll open a PR to fix this soon. Currently, the [neighborhood analysis notebook](https://github.com/angelolab/ark-analysis/blob/main/templates/example_neighborhood_analysis_script.ipynb) allows users to examine functional marker expression within...

Oh I see what you mean. The neighborhood analysis only looks at average marker expression not considering the binary functional positivity. Currently there is no next step within ark itself,...