imaging-server-kit 0.0.2__tar.gz → 0.0.3__tar.gz

{imaging_server_kit-0.0.2 → imaging_server_kit-0.0.3}/Dockerfile-registry

@@ -1,4 +1,4 @@
-FROM registry.rcp.epfl.ch/imaging-server-kit/imaging-server-kit:3.9
+FROM mallorywittwerepfl/imaging-server-kit:3.9
 
 COPY start_registry.py .
 

{imaging_server_kit-0.0.2 → imaging_server_kit-0.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: imaging-server-kit
-Version: 0.0.2
+Version: 0.0.3
 Summary: Deploy image processing algorithms in FastAPI servers. 
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License: Copyright (c) 2024, EPFL
@@ -54,92 +54,122 @@ Requires-Dist: tifffile
 Requires-Dist: numpy
 Requires-Dist: scikit-image
 Requires-Dist: geojson
-Requires-Dist: docker
 Requires-Dist: jinja2
 Requires-Dist: pyyaml
 Requires-Dist: dash
 Requires-Dist: dash-bootstrap-components
+Requires-Dist: a2wsgi
 Requires-Dist: pytest
 
 ![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
 # 🪐 Imaging Server Kit
 
-Run seamlessly interoperable algorithms on images using FastAPI.
+Deploy image processing algorithms in FastAPI servers and easily run them in Napari, QuPath, and more.
 
-## Setup
-
-Build the `imaging-server-kit` image with `docker`:
+## Usage
 
-```
-docker build -t imaging-server-kit:3.9 .
+### Algorithm servers
+
+Set up and run a server with one, or multiple algorithms from the Imaging Server Kit collection (or your own):
+
+- [StarDist](https://github.com/Imaging-Server-Kit/serverkit-stardist)
+- [CellPose](https://github.com/Imaging-Server-Kit/serverkit-cellpose)
+- [Spotiflow](https://github.com/Imaging-Server-Kit/serverkit-spotiflow)
+- [Rembg](https://github.com/Imaging-Server-Kit/serverkit-rembg)
+- [Scikit-image LoG detector](https://github.com/Imaging-Server-Kit/serverkit-skimage-LoG)
+- [Orientationpy](https://github.com/Imaging-Server-Kit/serverkit-orientationpy)
+<!-- - [Tau Fibrils Detector](https://github.com/Imaging-Server-Kit/serverkit-tau-fibrils-yolo) -->
+
+To do that, the recommended way is to edit a `docker-compose.yml` file and pull server images from `registry.rcp.epfl.ch` (EPFL users only):
+
+```{docker-compose.yml}
+services:
+  servers_registry:
+    image: mallorywittwerepfl/imaging-server-kit:registry
+    ports:
+      - "8000:8000"
+  rembg:
+    image: registry.rcp.epfl.ch/imaging-server-kit/serverkit-rembg:latest
+    depends_on:
+      - servers_registry
+  skimage-log:
+    image: registry.rcp.epfl.ch/imaging-server-kit/serverkit-skimage-log:latest
+    depends_on:
+      - servers_registry
 ```
 
-or build specific images:
+Start the server with
 
 ```
-docker build -t imaging-server-kit:3.10 --file Dockerfile-3.10 .
-docker build -t imaging-server-kit:gpu --file Dockerfile-GPU .
+docker compose up
 ```
 
-**Run an algorithm server**
+The server should be accessible at http://localhost:8000.
 
-The server will be running on `http://localhost:8000`.
+**Build the docker images yourself**
 
-```bash
-docker build -t serverkit/rembg .
-docker run -it --rm -p 8000:8000 serverkit/rembg
-```
+To build the algorithm server images yourself (e.g. if you are not from EPFL), see [Reference Deployment](https://github.com/Imaging-Server-Kit/serverkit-deploy-docker).
 
-**Run an algorithm server with multiple algorithms**
+**Create a server for your project**
 
-See [deployment](./reference_deployment/README.md). The server will be running on `http://localhost:7000`.
+To learn how to create a server for your project, see [Algorithm Server Template](https://github.com/Imaging-Server-Kit/cookiecutter-serverkit).
 
-## Usage
-
-**Python client**
+### Python client
 
-Install the `imaging-server-kit` package with `pip`:
-
-```
-pip install git+https://gitlab.com/epfl-center-for-imaging/imaging-server-kit.git
-```
-
-Connect to an algorithm server and run algorithms from Python:
+Once the server is running, connect to it and run algorithms from Python:
 
 ```python
 from imaging_server_kit import Client
 
-client = Client()
-
-client.connect("http://localhost:7000")
+client = Client("http://localhost:8000")
 
 print(client.algorithms)
-# [`rembg`, `stardist`, `sam2`]
+# [`rembg`, `stardist`, `cellpose`]
 
-data_tuple = client.run_algorithm(
+algo_output = client.run_algorithm(
     algorithm="rembg",
     image=(...),
     rembg_model_name="silueta",
 )
 ```
 
-More [examples](./examples/).
+### Napari plugin
+
+Once the server is running, use the [Napari Server Kit](https://github.com/Imaging-Server-Kit/napari-serverkit) plugin to connect to it and run algorithms in Napari.
 
-**Napari client**
+### QuPath extension
 
-Coming soon.
+Once the server is running, use the [QuPath Extension Server Kit](https://github.com/Imaging-Server-Kit/qupath-extension-serverkit) to connect to it and run algorithms from within QuPath.
 
-**Web client**
+## Install locally
 
-Coming soon.
+Install the `imaging-server-kit` package with `pip`:
+
+```
+pip install imaging-server-kit
+```
 
-**QuPath client**
+or clone the project and install the development version:
+
+```
+git clone https://github.com/Imaging-Server-Kit/imaging-server-kit.git
+cd imaging-server-kit
+pip install -e .
+```
 
-Coming soon.
+## Build with `docker`
 
-**Fiji plugin**
+Build the `imaging-server-kit` docker image for a specific Python version:
 
-Coming soon.
+```
+docker build --build-arg PYTHON_VERSION=3.9 -t imaging-server-kit:3.9 .
+```
+
+Run [build.sh](./build.sh) to build docker images for Python 3.9, 3.10, 3.11, GPU and the server kit registry:
+
+```
+bash ./build.sh
+```
 
 ## Contributing
 

imaging_server_kit-0.0.3/README.md

@@ -0,0 +1,121 @@
+![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
+# 🪐 Imaging Server Kit
+
+Deploy image processing algorithms in FastAPI servers and easily run them in Napari, QuPath, and more.
+
+## Usage
+
+### Algorithm servers
+
+Set up and run a server with one, or multiple algorithms from the Imaging Server Kit collection (or your own):
+
+- [StarDist](https://github.com/Imaging-Server-Kit/serverkit-stardist)
+- [CellPose](https://github.com/Imaging-Server-Kit/serverkit-cellpose)
+- [Spotiflow](https://github.com/Imaging-Server-Kit/serverkit-spotiflow)
+- [Rembg](https://github.com/Imaging-Server-Kit/serverkit-rembg)
+- [Scikit-image LoG detector](https://github.com/Imaging-Server-Kit/serverkit-skimage-LoG)
+- [Orientationpy](https://github.com/Imaging-Server-Kit/serverkit-orientationpy)
+<!-- - [Tau Fibrils Detector](https://github.com/Imaging-Server-Kit/serverkit-tau-fibrils-yolo) -->
+
+To do that, the recommended way is to edit a `docker-compose.yml` file and pull server images from `registry.rcp.epfl.ch` (EPFL users only):
+
+```{docker-compose.yml}
+services:
+  servers_registry:
+    image: mallorywittwerepfl/imaging-server-kit:registry
+    ports:
+      - "8000:8000"
+  rembg:
+    image: registry.rcp.epfl.ch/imaging-server-kit/serverkit-rembg:latest
+    depends_on:
+      - servers_registry
+  skimage-log:
+    image: registry.rcp.epfl.ch/imaging-server-kit/serverkit-skimage-log:latest
+    depends_on:
+      - servers_registry
+```
+
+Start the server with
+
+```
+docker compose up
+```
+
+The server should be accessible at http://localhost:8000.
+
+**Build the docker images yourself**
+
+To build the algorithm server images yourself (e.g. if you are not from EPFL), see [Reference Deployment](https://github.com/Imaging-Server-Kit/serverkit-deploy-docker).
+
+**Create a server for your project**
+
+To learn how to create a server for your project, see [Algorithm Server Template](https://github.com/Imaging-Server-Kit/cookiecutter-serverkit).
+
+### Python client
+
+Once the server is running, connect to it and run algorithms from Python:
+
+```python
+from imaging_server_kit import Client
+
+client = Client("http://localhost:8000")
+
+print(client.algorithms)
+# [`rembg`, `stardist`, `cellpose`]
+
+algo_output = client.run_algorithm(
+    algorithm="rembg",
+    image=(...),
+    rembg_model_name="silueta",
+)
+```
+
+### Napari plugin
+
+Once the server is running, use the [Napari Server Kit](https://github.com/Imaging-Server-Kit/napari-serverkit) plugin to connect to it and run algorithms in Napari.
+
+### QuPath extension
+
+Once the server is running, use the [QuPath Extension Server Kit](https://github.com/Imaging-Server-Kit/qupath-extension-serverkit) to connect to it and run algorithms from within QuPath.
+
+## Install locally
+
+Install the `imaging-server-kit` package with `pip`:
+
+```
+pip install imaging-server-kit
+```
+
+or clone the project and install the development version:
+
+```
+git clone https://github.com/Imaging-Server-Kit/imaging-server-kit.git
+cd imaging-server-kit
+pip install -e .
+```
+
+## Build with `docker`
+
+Build the `imaging-server-kit` docker image for a specific Python version:
+
+```
+docker build --build-arg PYTHON_VERSION=3.9 -t imaging-server-kit:3.9 .
+```
+
+Run [build.sh](./build.sh) to build docker images for Python 3.9, 3.10, 3.11, GPU and the server kit registry:
+
+```
+bash ./build.sh
+```
+
+## Contributing
+
+Contributions are very welcome.
+
+## License
+
+This software is distributed under the terms of the [BSD-3](http://opensource.org/licenses/BSD-3-Clause) license.
+
+## Issues
+
+If you encounter any problems, please file an issue along with a detailed description.

{imaging_server_kit-0.0.2 → imaging_server_kit-0.0.3}/pyproject.toml

@@ -29,11 +29,11 @@ dependencies = [
     "numpy",
     "scikit-image",
     "geojson",
-    "docker",  # For the autostartup regsitry
     "jinja2",  # For the /info route
     "pyyaml",  # For the /info route
     "dash",  # For the dash app
     "dash-bootstrap-components",  # For the dash app
+    "a2wsgi",  # For the dash app
     "pytest",  # For testing
 ]
 

{imaging_server_kit-0.0.2 → imaging_server_kit-0.0.3}/src/imaging_server_kit/__init__.py

@@ -1,8 +1,12 @@
-from imaging_server_kit._version import __version__
+from ._version import version as __version__
+try:
+    from ._version import version as __version__
+except ImportError:
+    __version__ = "unknown"
+
 from imaging_server_kit.client import Client
 from imaging_server_kit.server import Server, Parameters
 from imaging_server_kit.registry import Registry
-from imaging_server_kit.autostartup_registry import AutoStartupRegistry
 from imaging_server_kit.encoding import encode_contents, decode_contents
 from imaging_server_kit.serialization import (
     serialize_result_tuple,

{imaging_server_kit-0.0.2 → imaging_server_kit-0.0.3}/src/imaging_server_kit/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.2'
-__version_tuple__ = version_tuple = (0, 0, 2)
+__version__ = version = '0.0.3'
+__version_tuple__ = version_tuple = (0, 0, 3)

{imaging_server_kit-0.0.2 → imaging_server_kit-0.0.3}/src/imaging_server_kit/client.py

@@ -52,7 +52,7 @@ class Client:
         algo_params_encoded = self._encode_numpy_parameters(algo_params)
 
         try:
-            endpoint = f"{self.server_url}/{algorithm}/"
+            endpoint = f"{self.server_url}/{algorithm}/process"
             response = requests.post(
                 endpoint,
                 json=algo_params_encoded,

{imaging_server_kit-0.0.2 → imaging_server_kit-0.0.3}/src/imaging_server_kit/registry.py

@@ -80,11 +80,11 @@ class Registry:
             response = requests.get(f"{algo_url}/")
             return response.json()
 
-        @self.app.post("/{algorithm}", status_code=status.HTTP_201_CREATED)
+        @self.app.post("/{algorithm}/process", status_code=status.HTTP_201_CREATED)
         async def run_algorithm(algorithm, request: Request):
             algo_url = self.services.get(algorithm)
             data = await request.json()
-            response = requests.post(f"{algo_url}/{algorithm}/", json=data)
+            response = requests.post(f"{algo_url}/{algorithm}/process", json=data)
             return response.json()
 
         @self.app.get("/{algorithm}/parameters")

{imaging_server_kit-0.0.2 → imaging_server_kit-0.0.3}/src/imaging_server_kit/server.py

@@ -11,7 +11,9 @@ from fastapi.staticfiles import StaticFiles
 from fastapi.templating import Jinja2Templates
 from imaging_server_kit.web_demo import generate_dash_app
 from pydantic import BaseModel, ConfigDict
-from starlette.middleware.wsgi import WSGIMiddleware
+from a2wsgi import WSGIMiddleware
+# from starlette.middleware.wsgi import WSGIMiddleware
+from contextlib import asynccontextmanager
 
 templates_dir = importlib.resources.files("imaging_server_kit").joinpath("templates")
 static_dir = importlib.resources.files("imaging_server_kit").joinpath("static")
@@ -47,7 +49,7 @@ class Server:
         self.algorithm_name = algorithm_name
         self.parameters_model = parameters_model
 
-        self.app = FastAPI(title=algorithm_name)
+        self.app = FastAPI(title=algorithm_name, lifespan=self.lifespan)
         self.app.mount("/static", StaticFiles(directory=str(static_dir)), name="static")
 
         # Set up the web demo app
@@ -63,14 +65,20 @@ class Server:
 
         self.app.mount(f"/{algorithm_name}/demo", WSGIMiddleware(dash_app.server))
 
-        self.app.on_event("startup")(self.register_with_registry)
-        self.app.on_event("shutdown")(self.deregister_from_registry)
+        # self.app.on_event("startup")(self.register_with_registry)
+        # self.app.on_event("shutdown")(self.deregister_from_registry)
 
         self.register_routes()
 
         self.services = [self.algorithm_name]
 
-    def register_with_registry(self):
+    @asynccontextmanager
+    async def lifespan(self, app: FastAPI):
+        await self.register_with_registry()
+        yield
+        await self.deregister_from_registry()
+
+    async def register_with_registry(self):
         try:
             response = requests.get(f"{REGISTRY_URL}/")
         except Exception:
@@ -89,7 +97,7 @@ class Server:
         else:
             print(f"Failed to register {self.algorithm_name}: {response.json()}")
 
-    def deregister_from_registry(self):
+    async def deregister_from_registry(self):
         deregister_url = f"{REGISTRY_URL}/deregister"
         response = requests.post(deregister_url, json={"name": self.algorithm_name})
         if response.status_code == 201:
@@ -124,7 +132,7 @@ class Server:
                 },
             )
 
-        @self.app.post(f"/{self.algorithm_name}/", status_code=status.HTTP_201_CREATED)
+        @self.app.post(f"/{self.algorithm_name}/process", status_code=status.HTTP_201_CREATED)
         async def run_algo(algo_params: self.parameters_model):
             result_data_tuple = self.run_algorithm(**algo_params.dict())
             serialized_results = serverkit.serialize_result_tuple(result_data_tuple)

imaging_server_kit-0.0.3/src/imaging_server_kit/static/index.css

@@ -0,0 +1,47 @@
+body {
+    font-family: Arial, sans-serif;
+    margin: 0;
+    padding: 0;
+    background-color: #f4f4f4;
+    color: #333;
+}
+.container {
+    max-width: 800px;
+    margin: 50px auto;
+    padding: 20px;
+    background-color: #fff;
+    box-shadow: 0 0 10px rgba(0, 0, 0, 0.1);
+    border-radius: 8px;
+}
+p {
+    line-height: 1.6;
+}
+a {
+    color: #333;
+    text-decoration: none;
+}
+
+.card-product {
+    border-radius: 5px;
+    overflow: hidden;
+    /* height: 80px; */
+    background: white;
+    /* box-shadow: 0 0 15px rgba(0,0,0,0.2); */
+    display: flex;
+    align-items: center;
+}
+
+.card-product h2 {
+    font-size: 16px;
+    font-weight: bold;
+    margin: 0;
+}
+
+.card-product .card-product-infos {
+    padding: 16px;
+}
+
+.card-product:hover {
+    background-color: #f4f4f4;
+}
+  

imaging_server_kit-0.0.3/src/imaging_server_kit/static/info.css

@@ -0,0 +1,124 @@
+body {
+    font-family: Arial, sans-serif;
+    margin: 0;
+    padding: 0;
+    background-color: #f4f4f4;
+    color: #333;
+}
+
+.container {
+    max-width: 800px;
+    margin: 50px auto;
+    padding: 20px;
+    background-color: #fff;
+    box-shadow: 0 0 10px rgba(0, 0, 0, 0.1);
+    border-radius: 8px;
+}
+
+p {
+    line-height: 1.6;
+}
+
+a {
+    color: #333;
+    text-decoration: none;
+}
+
+a:hover {
+    background-color: #f4f4f4;
+    border-radius: 5px;
+}
+
+.keyword {
+    border-radius: 2px;
+    background-color: #f4f4f4;
+    padding: 2px 4px;
+}
+
+.card-category {
+    flex-direction: column;
+    display: flex;
+    justify-content: center;
+    align-items: center;
+    font-size: 18px;
+    border-radius: 5px;
+}
+
+.card-category i {
+    font-size: 36px;
+    padding-top: 20px;
+}
+
+.cards {
+    display: grid;
+    grid-template-columns: 1fr 1fr 1fr;
+    grid-gap: 16px;
+}
+
+@media (min-width: 100px) and (max-width: 575px) {
+    .cards {
+        grid-template-columns: 1fr;
+    }
+}
+
+@media (min-width: 576px) {
+    .cards {
+        grid-template-columns: 1fr;
+    }
+}
+
+@media (min-width: 768px) {
+    .cards {
+        grid-template-columns: 1fr 1fr;
+    }
+}
+
+@media (min-width: 992px) {
+    .cards {
+        grid-template-columns: 1fr 1fr 1fr;
+    }
+}
+
+@media (min-width: 1200px) {
+    .cards {
+        grid-template-columns: 1fr 1fr 1fr;
+    }
+}
+
+table {
+    width: 100%;                 /* Make the table span the full width of its container */
+    border-collapse: collapse;   /* Remove gaps between table cells */
+    margin: 1rem 0;              /* Add some spacing above and below the table */
+    font-size: 0.9rem;           /* Slightly smaller font size for a subtle look */
+    color: #333;                 /* Dark gray text for readability */
+}
+
+thead {
+    color: #333;                 /* Ensure the text color contrasts well */
+    font-weight: bold;           /* Bold text for the header */
+    text-align: left;            /* Align text to the left for clarity */
+}
+
+thead th {
+    padding: 0.8rem;             /* Add padding for better spacing */
+    border-bottom: 1px solid #ddd; /* Subtle bottom border */
+}
+
+tbody tr {
+    border-bottom: 1px solid #ddd; /* Add borders between rows */
+}
+
+tbody td {
+    padding: 0.8rem;             /* Add padding for cell spacing */
+    vertical-align: top;         /* Align content to the top for readability */
+}
+
+tbody td:first-child {
+    font-weight: bold;           /* Emphasize the first column */
+    color: #555;                 /* Slightly darker text for the first column */
+}
+
+tbody td:last-child {
+    font-style: italic;          /* Italicize the last column for variation */
+    color: #666;                 /* Subtle gray for less prominent data */
+}

imaging_server_kit-0.0.3/src/imaging_server_kit/templates/index.html

@@ -0,0 +1,33 @@
+<!DOCTYPE html>
+<html lang="en">
+
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.2/dist/css/bootstrap.min.css" rel="stylesheet"
+        integrity="sha384-rbsA2VBKQat6jboKpBhxGzJLysoH5Wr1xEAWmupmCJA7D6hzBI7tWtK2p9jxX0/e" crossorigin="anonymous">
+    <link rel="stylesheet" href="/static/index.css">
+</head>
+
+<body>
+    <div class="container">
+        <h1>Running servers</h1>
+        {% for service in services %}
+        <a href="/{{ service }}/info">
+            <div class="card-product">
+                <div class="card-product-infos">
+                    <h2>{{ service }}</h2>
+                </div>
+            </div>
+        </a>
+        {% endfor %}
+    </div>
+    <script src="https://cdn.jsdelivr.net/npm/@popperjs/core@2.11.8/dist/umd/popper.min.js"
+        integrity="sha384-QFfYf8qpCIem7U+Uz5XYW6XPiA5sdP7ePLCTDBSMF0Os3J8nt9wM5L3yZGOI+73s"
+        crossorigin="anonymous"></script>
+    <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.2/dist/js/bootstrap.min.js"
+        integrity="sha384-Q8KdjMRRhHpXEmsdpu2x9NkRBe/HHU6hLmjNw07uGpD7jz1zPoj2a9t8WbQhAjc"
+        crossorigin="anonymous"></script>
+</body>
+
+</html>

imaging_server_kit-0.0.3/src/imaging_server_kit/templates/info.html

@@ -0,0 +1,78 @@
+<!DOCTYPE html>
+<html lang="en">
+
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.2/dist/css/bootstrap.min.css" rel="stylesheet"
+        integrity="sha384-rbsA2VBKQat6jboKpBhxGzJLysoH5Wr1xEAWmupmCJA7D6hzBI7tWtK2p9jxX0/e" crossorigin="anonymous">
+    <link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.0/css/all.min.css" rel="stylesheet">
+    <link rel="stylesheet" href="/static/info.css">
+</head>
+
+<body>
+    <div class="container">
+        <h1>{{ algo_info.project_name }}</h1>
+
+        <p>{{ algo_info.description }}</p>
+
+        <p><strong>Keywords:</strong>
+            {% for used_for_tag in algo_info.used_for %}
+            <span class="keyword">{{ used_for_tag }}</span>
+            {% endfor %}
+            {% for tag in algo_info.tags %}
+            <span class="keyword">{{ tag }}</span>
+            {% endfor %}
+        </p>
+
+        <div class="cards">
+            <a href="{{ algo_info.project_url }}">
+                <div class="card-category">
+                    <i class="fa-solid fa-house"></i>
+                    <p>Project Homepage</p>
+                </div>
+            </a>
+            <a href="{{ algo_info.serverkit_repo_url }}">
+                <div class="card-category">
+                    <i class="fa-brands fa-github"></i>
+                    <p>Server Kit Repository</p>
+                </div>
+            </a>
+            <a href="/demo">
+                <div class="card-category">
+                    <i class="fa-solid fa-rocket"></i>
+                    <p>Web demo</p>
+                </div>
+            </a>
+        </div>
+
+        <!-- <h3><strong>Parameters</strong></h3> -->
+        <table>
+            <thead>
+                <tr>
+                    <th>Parameter</th>
+                    <th></th>
+                    <th>Default</th>
+                </tr>
+            </thead>
+            <tbody>
+                {% for key, val in algo_params.items() %}
+                <tr>
+                    <td>{{ key }}</td>
+                    <td>{{ val.get("description") }}</td>
+                    <td>{{ val.get("default") }}</td>
+                </tr>
+                {% endfor %}
+            </tbody>
+        </table>
+    </div>
+    <script src="https://cdn.jsdelivr.net/npm/@popperjs/core@2.11.8/dist/umd/popper.min.js"
+        integrity="sha384-QFfYf8qpCIem7U+Uz5XYW6XPiA5sdP7ePLCTDBSMF0Os3J8nt9wM5L3yZGOI+73s"
+        crossorigin="anonymous"></script>
+    <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.2/dist/js/bootstrap.min.js"
+        integrity="sha384-Q8KdjMRRhHpXEmsdpu2x9NkRBe/HHU6hLmjNw07uGpD7jz1zPoj2a9t8WbQhAjc"
+        crossorigin="anonymous"></script>
+
+</body>
+
+</html>

{imaging_server_kit-0.0.2 → imaging_server_kit-0.0.3}/src/imaging_server_kit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: imaging-server-kit
-Version: 0.0.2
+Version: 0.0.3
 Summary: Deploy image processing algorithms in FastAPI servers. 
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License: Copyright (c) 2024, EPFL
@@ -54,92 +54,122 @@ Requires-Dist: tifffile
 Requires-Dist: numpy
 Requires-Dist: scikit-image
 Requires-Dist: geojson
-Requires-Dist: docker
 Requires-Dist: jinja2
 Requires-Dist: pyyaml
 Requires-Dist: dash
 Requires-Dist: dash-bootstrap-components
+Requires-Dist: a2wsgi
 Requires-Dist: pytest
 
 ![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
 # 🪐 Imaging Server Kit
 
-Run seamlessly interoperable algorithms on images using FastAPI.
+Deploy image processing algorithms in FastAPI servers and easily run them in Napari, QuPath, and more.
 
-## Setup
-
-Build the `imaging-server-kit` image with `docker`:
+## Usage
 
-```
-docker build -t imaging-server-kit:3.9 .
+### Algorithm servers
+
+Set up and run a server with one, or multiple algorithms from the Imaging Server Kit collection (or your own):
+
+- [StarDist](https://github.com/Imaging-Server-Kit/serverkit-stardist)
+- [CellPose](https://github.com/Imaging-Server-Kit/serverkit-cellpose)
+- [Spotiflow](https://github.com/Imaging-Server-Kit/serverkit-spotiflow)
+- [Rembg](https://github.com/Imaging-Server-Kit/serverkit-rembg)
+- [Scikit-image LoG detector](https://github.com/Imaging-Server-Kit/serverkit-skimage-LoG)
+- [Orientationpy](https://github.com/Imaging-Server-Kit/serverkit-orientationpy)
+<!-- - [Tau Fibrils Detector](https://github.com/Imaging-Server-Kit/serverkit-tau-fibrils-yolo) -->
+
+To do that, the recommended way is to edit a `docker-compose.yml` file and pull server images from `registry.rcp.epfl.ch` (EPFL users only):
+
+```{docker-compose.yml}
+services:
+  servers_registry:
+    image: mallorywittwerepfl/imaging-server-kit:registry
+    ports:
+      - "8000:8000"
+  rembg:
+    image: registry.rcp.epfl.ch/imaging-server-kit/serverkit-rembg:latest
+    depends_on:
+      - servers_registry
+  skimage-log:
+    image: registry.rcp.epfl.ch/imaging-server-kit/serverkit-skimage-log:latest
+    depends_on:
+      - servers_registry
 ```
 
-or build specific images:
+Start the server with
 
 ```
-docker build -t imaging-server-kit:3.10 --file Dockerfile-3.10 .
-docker build -t imaging-server-kit:gpu --file Dockerfile-GPU .
+docker compose up
 ```
 
-**Run an algorithm server**
+The server should be accessible at http://localhost:8000.
 
-The server will be running on `http://localhost:8000`.
+**Build the docker images yourself**
 
-```bash
-docker build -t serverkit/rembg .
-docker run -it --rm -p 8000:8000 serverkit/rembg
-```
+To build the algorithm server images yourself (e.g. if you are not from EPFL), see [Reference Deployment](https://github.com/Imaging-Server-Kit/serverkit-deploy-docker).
 
-**Run an algorithm server with multiple algorithms**
+**Create a server for your project**
 
-See [deployment](./reference_deployment/README.md). The server will be running on `http://localhost:7000`.
+To learn how to create a server for your project, see [Algorithm Server Template](https://github.com/Imaging-Server-Kit/cookiecutter-serverkit).
 
-## Usage
-
-**Python client**
+### Python client
 
-Install the `imaging-server-kit` package with `pip`:
-
-```
-pip install git+https://gitlab.com/epfl-center-for-imaging/imaging-server-kit.git
-```
-
-Connect to an algorithm server and run algorithms from Python:
+Once the server is running, connect to it and run algorithms from Python:
 
 ```python
 from imaging_server_kit import Client
 
-client = Client()
-
-client.connect("http://localhost:7000")
+client = Client("http://localhost:8000")
 
 print(client.algorithms)
-# [`rembg`, `stardist`, `sam2`]
+# [`rembg`, `stardist`, `cellpose`]
 
-data_tuple = client.run_algorithm(
+algo_output = client.run_algorithm(
     algorithm="rembg",
     image=(...),
     rembg_model_name="silueta",
 )
 ```
 
-More [examples](./examples/).
+### Napari plugin
+
+Once the server is running, use the [Napari Server Kit](https://github.com/Imaging-Server-Kit/napari-serverkit) plugin to connect to it and run algorithms in Napari.
 
-**Napari client**
+### QuPath extension
 
-Coming soon.
+Once the server is running, use the [QuPath Extension Server Kit](https://github.com/Imaging-Server-Kit/qupath-extension-serverkit) to connect to it and run algorithms from within QuPath.
 
-**Web client**
+## Install locally
 
-Coming soon.
+Install the `imaging-server-kit` package with `pip`:
+
+```
+pip install imaging-server-kit
+```
 
-**QuPath client**
+or clone the project and install the development version:
+
+```
+git clone https://github.com/Imaging-Server-Kit/imaging-server-kit.git
+cd imaging-server-kit
+pip install -e .
+```
 
-Coming soon.
+## Build with `docker`
 
-**Fiji plugin**
+Build the `imaging-server-kit` docker image for a specific Python version:
 
-Coming soon.
+```
+docker build --build-arg PYTHON_VERSION=3.9 -t imaging-server-kit:3.9 .
+```
+
+Run [build.sh](./build.sh) to build docker images for Python 3.9, 3.10, 3.11, GPU and the server kit registry:
+
+```
+bash ./build.sh
+```
 
 ## Contributing
 

{imaging_server_kit-0.0.2 → imaging_server_kit-0.0.3}/src/imaging_server_kit.egg-info/SOURCES.txt

@@ -15,7 +15,6 @@ start_registry.py
 examples/.gitkeep
 src/imaging_server_kit/__init__.py
 src/imaging_server_kit/_version.py
-src/imaging_server_kit/autostartup_registry.py
 src/imaging_server_kit/client.py
 src/imaging_server_kit/encoding.py
 src/imaging_server_kit/errors.py

{imaging_server_kit-0.0.2 → imaging_server_kit-0.0.3}/src/imaging_server_kit.egg-info/requires.txt

@@ -5,9 +5,9 @@ tifffile
 numpy
 scikit-image
 geojson
-docker
 jinja2
 pyyaml
 dash
 dash-bootstrap-components
+a2wsgi
 pytest

imaging_server_kit-0.0.2/README.md

@@ -1,91 +0,0 @@
-![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
-# 🪐 Imaging Server Kit
-
-Run seamlessly interoperable algorithms on images using FastAPI.
-
-## Setup
-
-Build the `imaging-server-kit` image with `docker`:
-
-```
-docker build -t imaging-server-kit:3.9 .
-```
-
-or build specific images:
-
-```
-docker build -t imaging-server-kit:3.10 --file Dockerfile-3.10 .
-docker build -t imaging-server-kit:gpu --file Dockerfile-GPU .
-```
-
-**Run an algorithm server**
-
-The server will be running on `http://localhost:8000`.
-
-```bash
-docker build -t serverkit/rembg .
-docker run -it --rm -p 8000:8000 serverkit/rembg
-```
-
-**Run an algorithm server with multiple algorithms**
-
-See [deployment](./reference_deployment/README.md). The server will be running on `http://localhost:7000`.
-
-## Usage
-
-**Python client**
-
-Install the `imaging-server-kit` package with `pip`:
-
-```
-pip install git+https://gitlab.com/epfl-center-for-imaging/imaging-server-kit.git
-```
-
-Connect to an algorithm server and run algorithms from Python:
-
-```python
-from imaging_server_kit import Client
-
-client = Client()
-
-client.connect("http://localhost:7000")
-
-print(client.algorithms)
-# [`rembg`, `stardist`, `sam2`]
-
-data_tuple = client.run_algorithm(
-    algorithm="rembg",
-    image=(...),
-    rembg_model_name="silueta",
-)
-```
-
-More [examples](./examples/).
-
-**Napari client**
-
-Coming soon.
-
-**Web client**
-
-Coming soon.
-
-**QuPath client**
-
-Coming soon.
-
-**Fiji plugin**
-
-Coming soon.
-
-## Contributing
-
-Contributions are very welcome.
-
-## License
-
-This software is distributed under the terms of the [BSD-3](http://opensource.org/licenses/BSD-3-Clause) license.
-
-## Issues
-
-If you encounter any problems, please file an issue along with a detailed description.

imaging_server_kit-0.0.2/src/imaging_server_kit/autostartup_registry.py

@@ -1,58 +0,0 @@
-from fastapi import FastAPI
-import docker
-
-class AutoStartupRegistry:
-    def __init__(self, algo_servers) -> None:
-        self.algo_servers = algo_servers
-        self.app = FastAPI()
-        self.app.on_event("shutdown")(self.stop_all_algorithm_containers)  # This doesn't work.
-        self.docker_client = docker.from_env()
-        self.services = {}
-        self.register_routes()
-    
-    def register_routes(self):
-        @self.app.get("/")
-        def home():
-            return list_services()
-
-        @self.app.get("/services")
-        def list_services():
-            return {"services": list(self.services.keys())}
-            
-        @self.app.get("/{algorithm}")
-        def get_algorithm_url(algorithm):
-            if algorithm not in self.services.keys():
-                container_url = self.start_algorithm_container(algorithm)
-            else:
-                container_url = self.services.get(algorithm).get("url")
-            return {"url": container_url}
-        
-    def start_algorithm_container(self, algorithm):
-        algorithm_server_image = self.algo_servers[algorithm].get('image')
-
-        port = self.algo_servers[algorithm].get('port')
-
-        container = self.docker_client.containers.run(
-            image=algorithm_server_image,
-            ports={"8000/tcp": port},
-            detach=True,
-            remove=True,
-            name=f"serverkit-server-{algorithm}"
-        )
-
-        container_url = f"http://localhost:{port}"
-
-        self.services[algorithm] = {
-            "container": container,
-            "url": container_url,
-        }
-
-        return container_url
-
-    def stop_algorithm_container(self, algorithm):
-        container = self.services[algorithm].get("container")
-        container.stop()
-    
-    def stop_all_algorithm_containers(self):
-        for algorithm in self.services.keys():
-            self.stop_algorithm_container(algorithm)    

imaging_server_kit-0.0.2/src/imaging_server_kit/static/index.css

@@ -1,32 +0,0 @@
-body {
-    font-family: Arial, sans-serif;
-    margin: 0;
-    padding: 0;
-    background-color: #f4f4f4;
-    color: #333;
-}
-.container {
-    max-width: 800px;
-    margin: 50px auto;
-    padding: 20px;
-    background-color: #fff;
-    box-shadow: 0 0 10px rgba(0, 0, 0, 0.1);
-    border-radius: 8px;
-}
-h1 {
-    color: #007BFF;
-}
-p {
-    line-height: 1.6;
-}
-a {
-    color: #007BFF;
-    text-decoration: none;
-}
-a:hover {
-    text-decoration: underline;
-}
-ul {
-    list-style-type: disc;
-    padding-left: 20px;
-}

imaging_server_kit-0.0.2/src/imaging_server_kit/static/info.css

@@ -1,32 +0,0 @@
-body {
-    font-family: Arial, sans-serif;
-    margin: 0;
-    padding: 0;
-    background-color: #f4f4f4;
-    color: #333;
-}
-.container {
-    max-width: 800px;
-    margin: 50px auto;
-    padding: 20px;
-    background-color: #fff;
-    box-shadow: 0 0 10px rgba(0, 0, 0, 0.1);
-    border-radius: 8px;
-}
-h1 {
-    color: #007BFF;
-}
-p {
-    line-height: 1.6;
-}
-a {
-    color: #007BFF;
-    text-decoration: none;
-}
-a:hover {
-    text-decoration: underline;
-}
-ul {
-    list-style-type: disc;
-    padding-left: 20px;
-}

imaging_server_kit-0.0.2/src/imaging_server_kit/templates/index.html

@@ -1,25 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
-
-<head>
-    <meta charset="UTF-8">
-    <meta name="viewport" content="width=device-width, initial-scale=1.0">
-    <link rel="stylesheet" href="/static/index.css">
-</head>
-
-<body>
-    <div class="container">
-        <h1>Running servers</h1>
-
-        <ul>
-            {% for service in services %}
-            <li>
-                <a href="/{{ service }}/info">{{ service }}</a>
-            </li>
-            {% endfor %}
-        </ul>
-
-    </div>
-</body>
-
-</html>

imaging_server_kit-0.0.2/src/imaging_server_kit/templates/info.html

@@ -1,63 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
-
-<head>
-    <meta charset="UTF-8">
-    <meta name="viewport" content="width=device-width, initial-scale=1.0">
-    <link rel="stylesheet" href="/static/info.css">
-</head>
-
-<body>
-    <div class="container">
-        <h1>{{ algo_info.project_name }}</h1>
-        <p>Package name: {{ algo_info.package_name }}</p>
-        <p>Serverkit project author: {{ algo_info.serverkit_author }}</p>
-        <p>Description: {{ algo_info.description }}</p>
-        <p><a href="{{ algo_info.project_url }}">Original Project</a></p>
-        <p><a href="{{ algo_info.serverkit_repo_url }}">ServerKit Repository</a></p>
-        <p><a href="/demo">Web demo</a></p>
-        <p>Used for:
-        <ul>
-            {% for used_for_tag in algo_info.used_for %}
-            <li>{{ used_for_tag }}</li>
-            {% endfor %}
-        </ul>
-        </p>
-        <p>Tags:
-        <ul>
-            {% for tag in algo_info.tags %}
-            <li>{{ tag }}</li>
-            {% endfor %}
-        </ul>
-        </p>
-        <p>Algorithm parameters:</p>
-        <table>
-            <thead>
-            <tr>
-                <th>Parameter</th>
-                <th>Title</th>
-                <th>Description</th>
-                <th>Type</th>
-                <th>Widget Type</th>
-                <th>Default</th>
-                <th>Required</th>
-            </tr>
-            </thead>
-            <tbody>
-            {% for key, val in algo_params.items() %}
-            <tr>
-                <td>{{ key }}</td>
-                <td>{{ val.get("title") }}</td>
-                <td>{{ val.get("description") }}</td>
-                <td>{{ val.get("type") }}</td>
-                <td>{{ val.get("widget_type") }}</td>
-                <td>{{ val.get("default") }}</td>
-                <td>{{ val.get("required") }}</td>
-            </tr>
-            {% endfor %}
-            </tbody>
-        </table>
-    </div>
-</body>
-
-</html>