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_sources/cosem_starter.rst.txt

@@ -0,0 +1,102 @@
+
+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`.
+
+.. code-block:: python
+
+    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:
+
+.. code-block:: python
+
+    # 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:
+
+.. code-block:: python
+
+    from dacapo.experiments.runs import RunConfig
+
+    run_config = RunConfig(
+        # other parameters...
+        start_config=start_config,
+    )
+
+Full Example
+------------
+
+Here’s how the complete setup looks:
+
+.. code-block:: python
+
+    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:
+
++-----------+----------------------------+-----------------+--------------------------------------------------------------+-----------+------------+-----------------+
+| 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.

_sources/index.rst.txt

@@ -13,6 +13,7 @@
    tutorial
    docker
    aws
+   cosem_starter
    autoapi/index
    cli