Fine-Tune Cosem Starter

The CosemStarter in DaCapo allows you to load a pretrained COSEM model and fine-tune it for your experiments. This guide explains how to set up and use CosemStarter in DaCapo.

Prerequisites

Ensure that you have DaCapo installed and configured correctly.

Step 1: Import the CosemStartConfig

To get started, you need to import CosemStartConfig from dacapo.experiments.starts.

from dacapo.experiments.starts import CosemStartConfig

Step 2: Configure the Start Model

The CosemStartConfig takes two parameters:

model_name: The name of the model setup to load.
checkpoint: The specific checkpoint ID to load the pretrained model from.

Example:

# We will now download a pretrained COSEM model and fine-tune from that model.
# It will only download the model the first time it is used.

start_config = CosemStartConfig("setup04", "1820500")

This configuration will download the COSEM model from setup setup04 and load the checkpoint 1820500. You only need to download the model once; subsequent runs will use the downloaded model.

Step 3: Create a Run with start_config

To start from the pretrained model, add start_config to your RunConfig. The RunConfig initializes the run and allows fine-tuning from the pretrained COSEM model.

Example:

from dacapo.experiments.runs import RunConfig

run_config = RunConfig(
    # other parameters...
    start_config=start_config,
)

Full Example

Here’s how the complete setup looks:

from dacapo.experiments.starts import CosemStartConfig
from dacapo.experiments.runs import RunConfig

# Define the start configuration to load the pretrained COSEM model
start_config = CosemStartConfig("setup04", "1820500")

# Define the run configuration with the start configuration
run_config = RunConfig(
    # other configurations,
    start_config=start_config,
)

# Now you can run this configuration in your experiment to start from the COSEM pretrained model

This setup will initiate your DaCapo run from the pretrained COSEM model and allow you to fine-tune it as needed.

Available COSEM Pretrained Models

Below is a table of the COSEM pretrained models available, along with their details:

Available COSEM Pretrained Models
Model	Checkpoints	Best Checkpoint	Classes	Input Res	Output Res	Model
setup04	975000, 625000, 1820500	1820500	ecs, pm, mito, mito_mem, ves, ves_mem, endo, endo_mem, er, er_mem, eres, nuc, mt, mt_out	8 nm	4 nm	Upsample U-Net
setup26.1	650000, 2580000	2580000	mito, mito_mem, mito_ribo	8 nm	4 nm	Upsample U-Net
setup28	775000	775000	er, er_mem	8 nm	4 nm	Upsample U-Net
setup36	500000, 1100000	1100000	nuc, nucleo	8 nm	4 nm	Upsample U-Net
setup45	625000, 1634500	1634500	ecs, pm	4 nm	4 nm	U-Net

Notes

The model will download only the first time you use it. After that, it will reuse the downloaded version.
Ensure that you have the necessary storage and access permissions configured for the COSEM model files.