Preparation for WebAtlas manuscript

[codecov-commenter]

Codecov Report

Patch coverage: 38.19% and project coverage change: -2.26 :warning:

Comparison is base (e285b98) 39.42% compared to head (12fbe3e) 37.17%.

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #70 +/- ## ========================================== - Coverage 39.42% 37.17% -2.26% ========================================== Files 10 14 +4 Lines 350 694 +344 ========================================== + Hits 138 258 +120 - Misses 212 436 +224 ``` | [Impacted Files](https://codecov.io/gh/haniffalab/webatlas-pipeline/pull/70?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab) | Coverage Δ | | |---|---|---| | [bin/\_\_init\_\_.py](https://codecov.io/gh/haniffalab/webatlas-pipeline/pull/70?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL19faW5pdF9fLnB5) | `100.00% <ø> (ø)` | | | [bin/build\_config.py](https://codecov.io/gh/haniffalab/webatlas-pipeline/pull/70?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL2J1aWxkX2NvbmZpZy5weQ==) | `0.00% <0.00%> (ø)` | | | [bin/constants.py](https://codecov.io/gh/haniffalab/webatlas-pipeline/pull/70?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL2NvbnN0YW50cy5weQ==) | `0.00% <ø> (ø)` | | | [bin/integrate\_anndata.py](https://codecov.io/gh/haniffalab/webatlas-pipeline/pull/70?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL2ludGVncmF0ZV9hbm5kYXRhLnB5) | `0.00% <0.00%> (ø)` | | | [bin/integrate\_image.py](https://codecov.io/gh/haniffalab/webatlas-pipeline/pull/70?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL2ludGVncmF0ZV9pbWFnZS5weQ==) | `0.00% <0.00%> (ø)` | | | [bin/process\_merscope.py](https://codecov.io/gh/haniffalab/webatlas-pipeline/pull/70?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL3Byb2Nlc3NfbWVyc2NvcGUucHk=) | `23.68% <23.68%> (ø)` | | | [bin/process\_xenium.py](https://codecov.io/gh/haniffalab/webatlas-pipeline/pull/70?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL3Byb2Nlc3NfeGVuaXVtLnB5) | `34.78% <34.78%> (ø)` | | | [bin/consolidate\_md.py](https://codecov.io/gh/haniffalab/webatlas-pipeline/pull/70?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL2NvbnNvbGlkYXRlX21kLnB5) | `92.85% <50.00%> (ø)` | | | [bin/generate\_image.py](https://codecov.io/gh/haniffalab/webatlas-pipeline/pull/70?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL2dlbmVyYXRlX2ltYWdlLnB5) | `58.33% <58.33%> (ø)` | | | [bin/process\_spaceranger.py](https://codecov.io/gh/haniffalab/webatlas-pipeline/pull/70?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL3Byb2Nlc3Nfc3BhY2VyYW5nZXIucHk=) | `58.06% <61.70%> (+27.29%)` | :arrow_up: | | ... and [4 more](https://codecov.io/gh/haniffalab/webatlas-pipeline/pull/70?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab)

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