nahual 0.0.4

Deploy and access image and data processing models across processes.

Nahual: Deploy and access image and data processing models across environments/processes.

Note that this is early work in progress.

This tool aims to provide a one-stop-shop source for multiple models to process imaging data or their derivatives. You can think of it as a much simpler ollama but for biological analyses, deep learning-based or otherwise.

Implemented tools

By default, the models and tools are deployable using Nix.

• trackastra: Transformer-based models trained on a multitude of datasets.
• DINOv2: Generalistic self-supervised model to obtain visual features.

WIP tools

• Baby: Segmentation, tracking and lineage assignment for budding yeast.
• Other models and methods (to be defined)

Usage

Step 1: Deploy server

cd to the model you want to deploy. In this case we will test the image embedding model DINOv2.

git clone https://github.com/afermg/dinov2.git
cd dinov2
nix develop --command bash -c "python server.py ipc:///tmp/example_name.ipc"

Step 2: Run client

Once the server is running, you can call it from a different python script.

import numpy

from nahual.client.dinov2 import load_model, process_data

address = "ipc:///tmp/example_name.ipc"

# Load models server-side
parameters = {"repo_or_dir": "facebookresearch/dinov2", "model": "dinov2_vits14_lc"}
load_model(parameters, address=address)

# Define custom data
data = numpy.random.random_sample((1, 3, 420, 420))
result = process_data(data, address=address)

You can press C-c C-c from the terminal where the server lives to kill it. We will also add a way to kill the server from within the client.

Adding support for new models

Any model requires a thin layer that communicates using nng. You can see an example of trackastra's server and client.

Roadmap

• Support multiple instances of a model loaded on memory server-side.
• Formalize supported packet formats: (e.g., numpy arrays, dictionary).
• Increase number of supported models/methods.
• Document server-side API.
• Integrate into the aliby pipelining framework.
• Support containers that wrap the Nix derivations.

Why nahual?

In Mesoamerican folklore, a Nahual is a shaman able to transform into different animals.