DINO4Cells_analysis

This repo will contain the code for reproducing the results and figures of the paper Unbiased single-cell morphology with self-supervised vision transformers .

For the code to train the model, go to https://github.com/broadinstitute/Dino4Cells_code.

Installation

pip install torch==1.12.1+cu116 torchvision==0.13.1+cu116 torchaudio==0.12.1 --extra-index-url https://download.pytorch.org/whl/cu116

pip install -r requirements.py

Typical installation time: 10 minutes

Classification

To train classifiers on the features extracted using DINO, please use the following pipeline for the different datasets and tasks:

For each dataset, we want to publish:

DINO model checkpoints metadata features embeddings classifiers misc (data partition indices, preprocessed data, etc.)

Typical running time: 1 hour

The expected output of the code is shown inside the jupyter notebooks

Data

HPA FOV

For the HPA FOV data, access https://zenodo.org/record/8061392

Model checkpoints

HPAFOVdata/DINOFOVcheckpoint.pth

HPAFOVdata/densenetmodelbatch.onnx

HPAFOVdata/densenet_model.onnx

metadata

HPAFOVdata/whole_images.csv

features

HPAFOVdata/DINOfeaturesforHPAFOV.pth

HPAFOVdata/bestfittingfeaturesforHPAFOV.pth

HPAFOVdata/pretrainedDINOfeaturesforHPA_FOV.pth

Embeddings

HPAFOVdata/DINOFOVharmonized_embeddings.csv

HPAFOVdata/DINOFOVembeddings.csv

Classifiers

HPAFOVdata/classifier_cells.pth

HPAFOVdata/classifier_proteins.pth

Misc

train / test divisions for protein localizations and cell line classification

HPAFOVdata/cellstrainIDs.pth

HPAFOVdata/cellsvalidIDs.pth

HPAFOVdata/train_IDs.pth

HPAFOVdata/valid_IDs.pth

HPA single cell kaggle protein localization competition, download from https://www.kaggle.com/competitions/human-protein-atlas-image-classification/leaderboard

HPAFOVdata/human-protein-atlas-image-classification-publicleaderboard.csv

HPA cell line RNASeq data

HPAFOVdata/rna_cellline.tsv

HPA FOV color visualization

HPAFOVdata/wholeimagecellcolorindices.pth

HPAFOVdata/wholeimageproteincolorindices.pth

HPA single cells

For the HPA single cell data, access https://zenodo.org/record/8061426

Model checkpoints

HPAsinglecellsdata/DINOsinglecellcheckpoint.pth

HPAsinglecellsdata/HPAsinglecellmodel_checkpoint.pth

HPAsinglecellsdata/dualheadconfig.json

HPAsinglecellsdata/dualheadmatched_state.pth

metadata

HPAsinglecellsdata/fixedsizemaskedsinglecellsfor_sc.csv

features

HPAsinglecellsdata/DINOfeaturesforHPAsinglecells.pth

HPAsinglecellsdata/dualheadfeaturesforHPAsinglecells.pth

HPAsinglecellsdata/pretrainedDINOfeaturesforHPAsingle_cells.pth

Embeddings

HPAsinglecellsdata/DINOembeddingaverageumap.csv

HPAsinglecellsdata/DINOharmonizedembeddingaverage_umap.csv

Classifiers

HPAsinglecellsdata/classifiercells.pth

HPAsinglecellsdata/classifierproteins.pth

Misc

HPA single cell kaggle protein localization competition, download from https://www.kaggle.com/competitions/hpa-single-cell-image-classification/leaderboard

HPAsinglecells_data/hpa-single-cell-image-classification-publicleaderboard.csv

HPA XML data

HPAsinglecellsdata/XMLHPA.csv

UNIPROT interaction dataset

HPAsinglecellsdata/uniportinteractions.tsv

HPA gene heterogeneity annotated by experts

HPAsinglecellsdata/geneheterogeneity.tsv

single cell metadata with genetic information

HPAsinglecellsdata/MasterscKaggle.csv

HPA single cell color visualization

HPAsinglecellsdata/cellcolor_indices.pth

HPAsinglecellsdata/proteincolor_indices.pth

WTC11

For the WTC11 data, access https://zenodo.org/record/8061424

Model checkpoints

WTC11data/DINOcheckpoint.pth

metadata

WTC11data/normalizedcell_df.csv

features

WTC11data/DINOfeaturesanddf.pth

WTC11data/engineeredfeatures.pth

WTC11data/pretrainedfeaturesanddf.pth

Embeddings

WTC11data/DINOtrained_embedding.pth

WTC11data/DINOtrainedharmonizedembedding.pth

WTC11data/pretrainedembedding.pth

WTC11data/pretrainedharmonized_embedding.pth

WTC11data/engineeredembedding.pth

Classifiers

WTC11data/predictionsforWTC11trained_model.pth

WTC11data/predictionsforWTC11pretrained_model.pth

WTC11data/predictionsforWTC11xgb.pth

Misc

WTC11data/trainindices.pth

WTC11data/testindices.pth

Cell Painting

For the Cell Painting data, access https://zenodo.org/record/8061428

DINO model checkpoints

CellPaintingdata/DINOcellpaintingbasecheckpoint.pth

CellPaintingdata/DINOcellpaintingsmallcheckpoint.pth

metadata and embeddings

CellPaintingdata/LINCSViTSmallCompresseddfandUMAP.csv

CellPaintingdata/CombinedCPdfandUMAP.csv

features

Code to calculate the PUMA results is in: https://github.com/CaicedoLab/2023MoshkovNatComm

misc (data partition indices, preprocessed data, etc.)

CellPaintingdata/scaffoldmedianpython_dino.csv