Resources

Refer to downloading from Google Cloud storage.

Example configuration YAMLs

Preprocessing YAML configuration sample file

gs://broad-dsp-cellmincer-data/configs/preprocess/optosynth.yaml

Training YAML configuration sample file

gs://broad-dsp-cellmincer-data/configs/train/default.yaml

Please modify these YAML files as appropriate for your run. The complete preprocessing and training YAML configuration options and their descriptions can be found under Resources.

Trained models

Pretrained CellMincer model on 5 Optosynth datasets simulated with \(Q=50\) photons per fluorophore, which can be found here. See our preprint for a detailed explanation of the Optosynth data generation process.

gs://broad-dsp-cellmincer-data/models/optosynth.ckpt

Pretrained CellMincer model on 10 Optopatch datasets, which can be found here. [1]

gs://broad-dsp-cellmincer-data/models/optopatch10.ckpt

Pretrained CellMincer model on 26 Optopatch datasets using BeRST fluorescence, which can be found here. [2]

gs://broad-dsp-cellmincer-data/models/pairedberst.ckpt

Footnotes

[1]

Data provided by Sami Farhi, Spatial Technology Platform (STP), Broad Institute of MIT and Harvard.

[2]

Data provided by Evan Miller, Departments of Molecular & Cell Biology and Chemistry and Helen Wills Neuroscience Institute, UC Berkeley.