Getting started

Run your first algorithm server

With the imaging-server-kit package installed, run:

serverkit demo

This will start a demo web server for a simple intensity threshold algorithm.

The server will be running on http://localhost:8000. Open your web browser and navigate to this page to check that the server is running. You should see a web page displaying information about the threshold algorithm server.

Usage from Napari

Now that the server is running, you can interact with it from different client apps. For usage in Napari, you need to install napari and the napari-serverkit plugin.

You can install the napari-serverkit plugin with pip:

pip install napari-serverkit

Then, start Napari with the plugin:

napari -w napari-serverkit

or open the plugin from Plugins > Server Kit (Napari Server Kit) in Napari.

With your server still running on http://localhost:8000, you should be able to connect to it, load a sample image, run the threshold algorithm on it, and have the results displayed in the viewer.

Usage from QuPath

You can also interact with the algorithm server via QuPath. To try it out, you need to install the qupath-extension-serverkit.

Usage from Python

It is also possible to connect to an algorithm server and run computations from Python directly:

from imaging_server_kit import Client

# Connect to the server
client = Client("http://localhost:8000")

# run_algorithm returns a list of data tuples
results = client.run_algorithm(
    algorithm="intensity-threshold", 
    image=image, 
    threshold=0.5,
)

# Unpack the first result data tuple
mask, result_metadata, result_type = results[0]

# Segmentaiton mask
print(mask.shape)