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Update S3 paths to match updated quilt datasets #56

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Merged
chantelleleveille merged 2 commits into from
Dec 9, 2024
Merged

Update S3 paths to match updated quilt datasets #56

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f605f60
update quilt paths on dev branch
chantelleleveille Dec 9, 2024
550b251
update dev readme
chantelleleveille Dec 9, 2024
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2 changes: 2 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@
# Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories
The `dev` branch reflects the most up to date version of this analysis. To exactly reproduce the analysis as seen in bioRxiv manuscript use the `bioRxiv-v1`.

The code in this repository generates all of the figures for Dixon et al. 2024 [(bioRxiv)](https://www.biorxiv.org/content/10.1101/2024.06.28.601071v1). It is primarily intended to support reproducibility of our research. In addition, researchers may find parts of this code valuable for future work.


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6 changes: 3 additions & 3 deletions nuc_morph_analysis/lib/preprocessing/all_datasets.py
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Expand Up @@ -23,7 +23,7 @@
# FMS ID for 2024-07-08_main_manifest.parquet generated from morflowgenesis v0.3.0
# with generate_main_manifest.py at commit 6e9eb0962343113ab3999ce6b59d8331ddab9a45
"fmsid": "443ac819f633494f936ff410c14c21ed", # morflowgenesis v0.3.0 updated with new density from watershed PR (9/19/24)
"s3_path": INTERMEDIATE_MANIFEST_DIR / "2024-06-25_baseline_intermediate_manifest.parquet",
"s3_path": INTERMEDIATE_MANIFEST_DIR / "2024-09-19_baseline_intermediate_manifest.parquet",
"pixel_size": PIXEL_SIZE_YX_100x,
"time_interval": 5, # min
"length_threshold": 10.0, # hours,
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# with generate_perturbation_manifest.py at commit ebe76b5e84c9ca24617e4d04aed8acc1c2c3bb62
"fmsid": "f95429aa9d084a699d9e591afd2f7792", # morflowgenesis v 0.3.0 updated with new density from density_calc PR (12/5/24)
"s3_path": INTERMEDIATE_MANIFEST_DIR
/ "2024-06-14_feeding_control_intermediate_manifest.parquet",
/ "2024-12-05_feeding_control_intermediate_manifest.parquet",
"pixel_size": PIXEL_SIZE_YX_100x,
"time_interval": 5, # min
"length_threshold": 10.0, # hours,
Expand All @@ -51,7 +51,7 @@
# with generate_perturbation_manifest.py at commit 725ed45a6413391b9927610649e6209c04bcae9f
"fmsid": "5e8170e7881a4ad09c236e3e0c056d75", # morflowgenesis v 0.3.0 updated with new density from density_calc PR (12/5/24)
"s3_path": INTERMEDIATE_MANIFEST_DIR
/ "2024-06-24_inhibitor_perturbation_intermediate_manifest.parquet",
/ "2024-12-05_inhibitor_perturbation_intermediate_manifest.parquet",
"pixel_size": PIXEL_SIZE_YX_100x,
"time_interval": 5, # min
"length_threshold": 10.0, # hours,
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