Closed shntnu closed 12 months ago
cellpainting-gallery
└── cpg0019-moshkov-deepprofiler
└──broad
└── training_images
│ ├── TAORF
│ │ └── images
│ │ └── <plate-id>
│ │ └── <well>
│ │ └── <site>
│ │ ├── <cell1>
│ │ ├── <cell2>
│ │ ├── ...
│ │ └── <celln>
│ ├── BBBC022
│ ├── LUAD
│ ├── CDRP
│ └── LINCS
└── workspace
Hi Shantanu, I have this folder structure now, any concerns or suggestions?
cpg0019-moshkov-deepprofiler
└── broad
├── training_images
│ ├── BBBC022
│ │ ├── A01
│ │ ├── 1
│ │ ├── *.png
│ ├── BBBC036
│ ├── BBBC037
│ ├── BBBC043
│ └── LINCS
└── workspace_dl
├── collated
│ └── 105281_zenodo7114558
│ ├── BBBC022
│ │ ├── notspherized.csv
│ │ └── spherized.csv
│ ├── BBBC036
│ │ ├── notspherized.csv
│ │ └── spherized.csv
│ └── BBBC037
│ ├── notspherized.csv
│ └── spherized.csv
├── consensus
│ └── 105281_zenodo7114558
│ ├── BBBC022
│ │ ├── notspherized.csv
│ │ └── spherized.csv
│ ├── BBBC036
│ │ ├── notspherized.csv
│ │ └── spherized.csv
│ └── BBBC037
│ ├── notspherized.csv
│ └── spherized.csv
├── embeddings
│ └── 105281_zenodo7114558
│ ├── BBBC022
│ │ ├── 20585
│ │ ├── A01
│ │ ├── 1
│ │ ├── embedding.npz
│ ├── BBBC036
│ └── BBBC037
└── metadata
├── BBBC022_profiling.csv
├── BBBC036_profiling.csv
├── BBBC037_profiling.csv
└── sc-metadata.csv
Looks great @Arkkienkeli!
I've modified https://github.com/broadinstitute/cellpainting-gallery/commit/c1412d605870350f512d093e229f39d0cd20c82a to reflect this
Hi @shntnu and @ErinWeisbart, is the dataset available in the gallery?
It is 🎉
@Arkkienkeli Are you happy with this one-liner to summarize cpg0019
?
8.3 million single cells from 232 plates, across 488 treatments from 5 public datasets, used for learning representations
Feel free to edit #27 if not.
I'm adding our email logs here for our records
Segmentation/ Feature extraction is being performed by (Cimini lab / Carpenter-Singh lab)
Profile creation is being performed by (Cimini lab / Carpenter-Singh lab)
Data can be public in RODA Immediately
Update as generated:
[Link to profile repo]
https://doi.org/10.1101/2022.08.12.503783
cpg0019-moshkov-deepprofiler
Transfer to CellPainting Gallery:
If data is being published, prepare for publication: These are only training images (crops)
Run Distributed-BioFormats2Raw to create .ome.zarr filesUpload (meta)data to IDR (images remain hosted in cellpainting-gallery).Once published: