cerebellum_setup11_nuc_32nm_190000

Fly StandardUnet model selected for cerebellum inference. Channel: nuc. Used for: jrc_mus-cerebellum-1 nuc, jrc_mus-cerebellum-3 nuc. Source YAMLs: /groups/cellmap/cellmap/zouinkhim/exp_cerebellum/inference/nuc/jrc_mus-cerebellum-1/run.yaml, /groups/cellmap/cellmap/zouinkhim/exp_cerebellum/inference/nuc/jrc_mus-cerebellum-3/run.yaml.

Model Details

Architecture	StandardUnet
Framework	torch
Spatial Dims	3
Input Channels	1
Output Channels	1
Channel Names	nuc
Iteration	190000
Input Voxel Size	32, 32, 32 nm
Output Voxel Size	32, 32, 32 nm
Inference Input Shape	378, 378, 378
Inference Output Shape	256, 256, 256

Available Formats

File	Format	Usage
model.pt	PyTorch pickle	torch.load("model.pt")
model.ts	TorchScript	torch.jit.load("model.ts")
model.onnx	ONNX	onnxruntime.InferenceSession("model.onnx")
metadata.json	JSON	Model metadata

Usage

pip install cellmap-models

from cellmap_models.model_export.cellmap_model import CellmapModel

model = CellmapModel("path/to/model/folder")

# Inference
output = model.ts_model(input_tensor)

# Finetuning
trainable_model = model.train()

Or download from this repo and load directly:

from huggingface_hub import snapshot_download
from cellmap_models.model_export.cellmap_model import CellmapModel

path = snapshot_download(repo_id="cerebellum_setup11_nuc_32nm_190000")
model = CellmapModel(path)

Author

CellMap Project Team, HHMI Janelia

Links

• cellmap-models
• CellMap Project