fly_organelles_run08_438000

Fly organelles segmentation model run08 iteration 438000

Model Details

Architecture	Sequential
Framework	torch
Spatial Dims	3
Input Channels	1
Output Channels	8
Channel Names	all_mem, organelle, mito, er, nucleus, pm, vs, ld
Iteration	438000
Input Voxel Size	8, 8, 8 nm
Output Voxel Size	8, 8, 8 nm
Inference Input Shape	178, 178, 178
Inference Output Shape	56, 56, 56

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="fly_organelles_run08_438000")
model = CellmapModel(path)

Author

Larissa Heinrich

Links

• cellmap-models
• CellMap Project