Tathey1 ailey

[tathey1]

Here I PR the code I use for my whole-brain light sheet image analysis pipeline. The main changes are:

• Add docs/notebooks/pipelines/lsm_analysis/axon_analysis.ipynb and docs/notebooks/pipelines/lsm_analysis/soma_analysis.ipynb which guide users through the pipeline
• Add several .py files to brainlit/lsm_analysis/ which constitute parts of the pipeline
• Test some of the utility code
• Add pipeline information to the docs
• Delete some useless files (notebooks and docs link stubs)
• reformat some files in docs/notebooks

[codecov[bot]]

Codecov Report

Merging #375 (4b04993) into develop (f5328ba) will increase coverage by 0.16%. The diff coverage is 91.09%.

:exclamation: Current head 4b04993 differs from pull request most recent head c94e6a9. Consider uploading reports for the commit c94e6a9 to get more accurate results

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #375 +/- ## =========================================== + Coverage 87.84% 88.00% +0.16% =========================================== Files 20 22 +2 Lines 2714 2860 +146 =========================================== + Hits 2384 2517 +133 - Misses 330 343 +13 ``` | [Impacted Files](https://codecov.io/gh/neurodata/brainlit/pull/375?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=neurodata) | Coverage Δ | | |---|---|---| | [brainlit/feature\_extraction/base.py](https://codecov.io/gh/neurodata/brainlit/pull/375?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=neurodata#diff-YnJhaW5saXQvZmVhdHVyZV9leHRyYWN0aW9uL2Jhc2UucHk=) | `69.93% <ø> (ø)` | | | [brainlit/napari\_viterbrain/viterbrain\_plugin.py](https://codecov.io/gh/neurodata/brainlit/pull/375?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=neurodata#diff-YnJhaW5saXQvbmFwYXJpX3ZpdGVyYnJhaW4vdml0ZXJicmFpbl9wbHVnaW4ucHk=) | `64.28% <ø> (ø)` | | | [brainlit/utils/upload.py](https://codecov.io/gh/neurodata/brainlit/pull/375?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=neurodata#diff-YnJhaW5saXQvdXRpbHMvdXBsb2FkLnB5) | `75.54% <ø> (ø)` | | | [brainlit/lsm\_analysis/parse\_ara.py](https://codecov.io/gh/neurodata/brainlit/pull/375?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=neurodata#diff-YnJhaW5saXQvbHNtX2FuYWx5c2lzL3BhcnNlX2FyYS5weQ==) | `88.88% <88.88%> (ø)` | | | [brainlit/lsm\_analysis/util.py](https://codecov.io/gh/neurodata/brainlit/pull/375?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=neurodata#diff-YnJhaW5saXQvbHNtX2FuYWx5c2lzL3V0aWwucHk=) | `92.77% <92.77%> (ø)` | |

[tathey1]

@PSSF23 could you do a quick review of this for me? No need to look at all the code, just make sure what I did generally follows the PR description. And maybe take a look at the new docs site to see if things look somewhat organized.

[tathey1]

@PSSF23 Thanks! I moved some imports and condensed a little code. But for now I think I'm going to keep the other stuff there because the goal is for the user to see most of the code that I use (rather than hide it), because they will likely be modifying things for their own workflow.