Tutorials | Fish1 Release

Programmatic Access to Fish1 Dataset

These tutorials guide you through using the CAVE (Connectome Annotation and Versioning Engine) to access and analyze the Fish1 dataset.

The links below open in the Jupyter Notebook viewer (read-only). To execute code, download the notebooks from VCG/cave-scripts or run them directly in Google Colab.

Setup CAVE

Local Machine

Download example notebooks from the repository:
Install the CAVE client: Please refer to the cave-scripts page for more details.
Configure your credentials following the CAVEclient documentation.

Google Colab

Go to File → Open Notebook → GitHub (at the left panel).
Search for: VCG/cave-scripts and open notebooks/fish1/Setup_CAVE.ipynb.
Add code cell and type command to install the CAVEclient package:
```
!pip install caveclient
```

Upload your Annotation Table

Choose a data schema and create an annotation table.
Upload your custom annotations to the table.

Query the Dataset

Query data from materialized annotation table.
Explore and analyze synapses querying by pre-synaptic or post-synaptic cells.

Use Cases

Lookup Root ID by Coordinates

def get_latest_root_id(x, y, z):
    supervoxel_id = cv.download_point(pt=(x, y, z), 
                                      size=1, 
                                      agglomerate=False, 
                                      coord_resolution=resolution)
    supervoxel_id = np.int64(supervoxel_id[0, 0, 0, 0]) 
    print(f"supervoxel_id: {supervoxel_id}")
    root_id = cggraph.get_root_id(supervoxel_id)
    print(f"root_id: {root_id}")
    is_latest = cggraph.is_latest_roots([root_id])
    if not is_latest:
        latest_root_id = cggraph.get_latest_roots(root_id)
        print(f"latest_root_id: {latest_root_id}")
    else:
        latest_root_id = root_id
        print("root_id is the latest")
    
    return supervoxel_id, root_id, latest_root_id

Example:

supervoxel_id, root_id, latest_root_id = get_latest_root_id(37880, 22443, 4595)

Decompressing: 100%|██████████| 1/1 [00:00<00:00, 389.84it/s] 

              supervoxel_id: 82407780375333845 

              root_id: 864691128652664051 

              root_id is the latest