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Fine-Tune Cosem Starter

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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.

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Prerequisites

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Ensure that you have DaCapo installed and configured correctly.

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Step 1: Import the CosemStartConfig

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

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from dacapo.experiments.starts import CosemStartConfig
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Step 2: Configure the Start Model

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The CosemStartConfig takes two parameters:

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  • model_name: The name of the model setup to load.

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  • checkpoint: The specific checkpoint ID to load the pretrained model from.

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Example:

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# 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.
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+start_config = CosemStartConfig("setup04", "1820500")
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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.

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Step 3: Create a Run with start_config

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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.

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Example:

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from dacapo.experiments.runs import RunConfig
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+run_config = RunConfig(
+    # other parameters...
+    start_config=start_config,
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Full Example

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Here’s how the complete setup looks:

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from dacapo.experiments.starts import CosemStartConfig
+from dacapo.experiments.runs import RunConfig
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+# Define the start configuration to load the pretrained COSEM model
+start_config = CosemStartConfig("setup04", "1820500")
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+# Define the run configuration with the start configuration
+run_config = RunConfig(
+    # other configurations,
+    start_config=start_config,
+)
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+# Now you can run this configuration in your experiment to start from the COSEM pretrained model
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This setup will initiate your DaCapo run from the pretrained COSEM model and allow you to fine-tune it as needed.

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Available COSEM Pretrained Models

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

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Notes

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  • The model will download only the first time you use it. After that, it will reuse the downloaded version.

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  • Ensure that you have the necessary storage and access permissions configured for the COSEM model files.

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