Export dacapo

[mzouink]

Used to export dacapo model

You can use the interactive script to export the model.:

dcc_dacapo

The exported folder will contain the following files:

<run_name>/
├── model.omnx
├── model.pt
├── model.ts
├── README.md
└── metadata.json

The metadata.json file contains the following model metadata structure:

{
    "model_name": "model_name",
    "model_type": "UNet",
    "framework": "Dacapo",
    "spatial_dims": 3,
    "in_channels": 1,
    "out_channels": 2,
    "iteration": 1000,
    "input_voxel_size": [8, 8, 8],
    "output_voxel_size": [8, 8, 8],
    "channels_names": ["CT", "PET"],
    "input_shape": [96, 96, 96],
    "output_shape": [96, 96, 96],
    "author": "author",
    "description": "description",
    "version": "1.0.0"
}

Attribute	Type	Description	Example
model_name	Optional[str]
model_type	Optional[str]	UNet or DenseNet121
framework	Optional[str]	Dacapo or PyTorch
spatial_dims	Optional[int]	2 or 3
in_channels	Optional[int]
out_channels	Optional[int]
iteration	Optional[int]
input_voxel_size	Optional[List[int]]	Comma-separated values	8,8,8
output_voxel_size	Optional[List[int]]	Comma-separated values	8,8,8
channels_names	Optional[List[str]]	Comma-separated values	'CT, PET'
input_shape	Optional[List[int]]	Comma-separated values	96,96,96
output_shape	Optional[List[int]]	Comma-separated values	96,96,96
author	Optional[str]
description	Optional[str]
version	Optional[str]		1.0.0

Saved models

jrc_mus_liver

• 8nm mito :

  • v21_mito_attention_finetuned_distances_8nm_mito_jrc_mus-livers_mito_8nm_attention-upsample-unet_default_one_label_1
  • iteration: 345000

• 8nm peroxisome :

  • v22_peroxisome_funetuning_best_v20_1e4_finetuned_distances_8nm_peroxisome_jrc_mus-livers_peroxisome_8nm_attention-upsample-unet_default_one_label_finetuning_0
  • iteration: 45000

Note: i had to checkout dacapo to version Feb 15 10:49:53 2024

commit 5371dedd3a008e438b601a227c4166273aab34bf

commit 5371dedd3a008e438b601a227c4166273aab34bf (HEAD)
Author: Marwan Zouinkhi <[email protected]>
Date:   Thu Feb 15 10:49:53 2024 -0500

    docstrings losses

dacapo.yaml

mongo_db_name: dacapo_cellmap_v3_zouinkhim
runs_base_dir: "/nrs/cellmap/zouinkhim/crop_num_experiment_v2"
mongo_db_host: mongodb://cellmapAdmin:LUwWXkSY8N3AqCcw@cellmap-mongo:27017
type: "mongo"

[mzouink]

@davidackerman @rhoadesScholar @krokicki
Can you check
for the models i will upload them to s3 with a loader from cellmap_models