talmolab · roomrys · Dec 16, 2024 · May 29, 2024 · May 29, 2024 · Jun 1, 2024
diff --git a/docs/_static/bonsai-connection.jpg b/docs/_static/bonsai-connection.jpg
diff --git a/docs/_static/bonsai-filecapture.jpg b/docs/_static/bonsai-filecapture.jpg
diff --git a/docs/_static/bonsai-predictcentroids.jpg b/docs/_static/bonsai-predictcentroids.jpg
diff --git a/docs/_static/bonsai-predictposeidentities.jpg b/docs/_static/bonsai-predictposeidentities.jpg
diff --git a/docs/_static/bonsai-predictposes.jpg b/docs/_static/bonsai-predictposes.jpg
diff --git a/docs/_static/bonsai-workflow.jpg b/docs/_static/bonsai-workflow.jpg
diff --git a/docs/guides/bonsai.md b/docs/guides/bonsai.md
@@ -0,0 +1,75 @@
+(bonsai)=
+
+# Using Bonsai with SLEAP
+
+Bonsai is a visual language for reactive programming and currently supports SLEAP models.
+
+:::{note}
+Currently Bonsai supports only single instance, top-down and top-down-id SLEAP models.
+:::
+
+### Exporting a SLEAP trained model
+
+Before we can import a trained model into Bonsai, we need to use the {code}`sleap-export` command to convert the model to a format supported by Bonsai. For example, to export a top-down-id model, the command is as follows:
+
+```bash
+sleap-export -m centroid/model/folder/path -m top_down_id/model/folder/path -e exported/model/path
+```
+
+Please refer to the {ref}`sleap-export` docs for more details on using the command.
+
+This will generate the necessary `.pb` file and other information files required by Bonsai. In this example, these files were saved to the specified `exported/model/path` folder.
+
+The `exported/model/path` folder will have a structure like the following:
+
+```plaintext
+exported/model/path
+├── centroid_config.json
+├── confmap_config.json
+├── frozen_graph.pb
+└── info.json
+```
+
+### Installing Bonsai and necessary packages
+
+1. Install Bonsai. See the [Bonsai installation instructions](https://bonsai-rx.org/docs/articles/installation.html). 
+
+2. Download and add the necessary packages for Bonsai to run with SLEAP. See the official [Bonsai SLEAP documentation](https://github.com/bonsai-rx/sleap?tab=readme-ov-file#bonsai---sleap) for more information.
+
+### Using Bonsai SLEAP modules
+
+Once you have Bonsai installed with the required packages, you should be able to open the Bonsai application. The workflow must have a source module `FileCapture` which can be found in the toolbox search in the workflow editor. Provide the path to the video that was used to train the SLEAP model in the `FileName` field of the module.
+
+![Bonsai FileCapture module](../_static/bonsai-filecapture.jpg)
+
+#### Top-down model
+The top-down model requires both the `PredictCentroids` and the `PredictPoses` modules.
+
+The `PredictCentroids` module will predict the centroids of detections. There are two fields inside the `PredictCentroids` module: the `ModelFileName` field and the `TrainingConfig` field. The `TrainingConfig` field expects the path to the training config JSON file for the centroid model. The `ModelFileName` field expects the path to the `frozen_graph.pb` file in the `exported/model/path` folder.
+
+![Bonsai PredictCentroids module](../_static/bonsai-predictcentroids.jpg)
+
+The `PredictPoses` module will predict the instances of detections. Similar to the `PredictCentroid` module, there are two fields inside the `PredictPoses` module: the `ModelFileName` field and the `TrainingConfig` field. The `TrainingConfig` field expects the path to the training config JSON file for the centered instance model. The `ModelFileName` field expects the path to the `frozen_graph.pb` file in the `exported/model/path` folder.
+
+![Bonsai PredictPoses module](../_static/bonsai-predictposes.jpg)
+
+#### Top-Down-ID model
+The `PredictPoseIdentities` module will predict the instances with identities. This module has two fields: the `ModelFileName` field and the `TrainingConfig` field. The `TrainingConfig` field expects the path to the training config JSON file for the top-down-id model. The `ModelFileName` field expects the path to the `frozen_graph.pb` file in the `exported/model/path` folder.
+
+![Bonsai PredictPoseIdentities module](../_static/bonsai-predictposeidentities.jpg)
+
+#### Single instance model
+The `PredictSinglePose` module will predict the poses for single instance models. This module also has two fields: the `ModelFileName` field and the `TrainingConfig` field. The `TrainingConfig` field expects the path to the training config JSON file for the single instance model. The `ModelFileName` field expects the path to the `frozen_graph.pb` file in the `exported/model/path` folder.
+
+### Connecting the modules
+Right-click on the `FileCapture` module and select **Create Connection**. Now click on the required SLEAP module to complete the connection. 
+
+![Bonsai module connection ](../_static/bonsai-connection.jpg)
+
+Once it is done, the workflow in Bonsai will look something like the following:
+
+![Bonsai.SLEAP workflow](../_static/bonsai-workflow.jpg)
+
+Now you can click the green start button to run the workflow and you can add more modules to analyze and visualize the results in Bonsai.
+
+For more documentation on various modules and workflows, please refer to the [official Bonsai docs](https://bonsai-rx.org/docs/articles/editor.html).
diff --git a/docs/guides/index.md b/docs/guides/index.md
@@ -30,6 +30,10 @@
 
 {ref}`remote-inference` when you trained models and you want to run inference on a different machine using a **command-line interface**.
 
+## SLEAP with Bonsai
+
+{ref}`bonsai` when you want to analyze the trained SLEAP model to visualize the poses, centroids and identities for further visual analysis.
+
 ```{toctree}
 :hidden: true
 :maxdepth: 2
@@ -44,4 +48,5 @@ proofreading
 colab
 custom-training
 remote
+bonsai
 ```