imaging-server-kit 0.0.12__tar.gz → 0.0.14__tar.gz

{imaging_server_kit-0.0.12 → imaging_server_kit-0.0.14}/.github/workflows/publish.yml

@@ -24,4 +24,13 @@ jobs:
         uses: pypa/gh-action-pypi-publish@v1.5.0
         with:
           user: __token__
-          password: ${{ secrets.TWINE_API_KEY }}
+          password: ${{ secrets.TWINE_API_KEY }}
+      - name: Create Release
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          tag: ${{ github.ref_name }}
+        run: |
+          gh release create "$tag" \
+            --repo="$GITHUB_REPOSITORY" \
+            --title="${GITHUB_REPOSITORY#*/} ${tag#v}" \
+            --generate-notes

{imaging_server_kit-0.0.12 → imaging_server_kit-0.0.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: imaging-server-kit
-Version: 0.0.12
+Version: 0.0.14
 Summary: Deploy image processing algorithms in FastAPI servers. 
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License: Copyright (c) 2024, EPFL

{imaging_server_kit-0.0.12 → imaging_server_kit-0.0.14}/docs/_toc.yml

@@ -4,8 +4,6 @@ chapters:
 - file: sections/getting_started
 - file: sections/algorithm_server
 - file: sections/multi_algo_server
-# - file: sections/client_apps
-# - file: sections/authentication
 - file: sections/docker
 - file: sections/examples
 - file: sections/api_endpoints

{imaging_server_kit-0.0.12 → imaging_server_kit-0.0.14}/docs/index.md

@@ -21,10 +21,10 @@ def segmentation_server(image):
 | Task              | Examples                        | Napari | QuPath |
 |-------------------|---------------------------------| ------ | ------ |
 | Segmentation     | [StarDist](https://github.com/Imaging-Server-Kit/imaging-server-kit/tree/main/examples/servers/serverkit-stardist), [CellPose](https://github.com/Imaging-Server-Kit/imaging-server-kit/tree/main/examples/servers/serverkit-cellpose), [Rembg](https://github.com/Imaging-Server-Kit/imaging-server-kit/tree/main/examples/servers/serverkit-rembg), [SAM-2](https://github.com/Imaging-Server-Kit/extra-examples/tree/main/examples/serverkit-sam2), [InstanSeg](https://github.com/Imaging-Server-Kit/extra-examples/tree/main/examples/serverkit-instanseg)               | ✅ | ✅ |
-| Object detection | [Spotiflow](https://github.com/Imaging-Server-Kit/extra-examples/tree/main/examples/serverkit-spotiflow), [LoG detector](https://github.com/Imaging-Server-Kit/imaging-server-kit/tree/main/examples/servers/serverkit-skimage-log)    | ✅ | ✅ |
+| Object detection | [YOLO](https://github.com/Imaging-Server-Kit/imaging-server-kit/tree/main/examples/servers/serverkit-yolo), [Spotiflow](https://github.com/Imaging-Server-Kit/extra-examples/tree/main/examples/serverkit-spotiflow), [LoG detector](https://github.com/Imaging-Server-Kit/imaging-server-kit/tree/main/examples/servers/serverkit-skimage-log)    | ✅ | ✅ |
 | Vector fields    | [Orientationpy](https://github.com/Imaging-Server-Kit/imaging-server-kit/tree/main/examples/servers/serverkit-orientationpy)                   | ✅ | ✅ |
 | Object tracking  | [Trackpy](https://github.com/Imaging-Server-Kit/imaging-server-kit/tree/main/examples/servers/serverkit-trackpy), [Trackastra]()         | ✅ |  |
-| Image-to-Image   | [SPAM](https://github.com/Imaging-Server-Kit/extra-examples/tree/main/examples/serverkit-spam), [Noise2Void](https://github.com/Imaging-Server-Kit/extra-examples/tree/main/examples/serverkit-n2v)         | ✅ |  |
+| Image-to-Image   | [SPAM](https://github.com/Imaging-Server-Kit/extra-examples/tree/main/examples/serverkit-spam), [Noise2Void](https://github.com/Imaging-Server-Kit/extra-examples/tree/main/examples/serverkit-n2v), [StackReg](https://github.com/Imaging-Server-Kit/imaging-server-kit/tree/main/examples/servers/serverkit-stackreg)         | ✅ |  |
 | Text-to-Image    | [Stable Diffusion](https://github.com/Imaging-Server-Kit/extra-examples/tree/main/examples/serverkit-stable-diffusion)         | ✅ |  |
 | Image-to-Text    | [Image captioning](https://github.com/Imaging-Server-Kit/extra-examples/tree/main/examples/serverkit-blip-captioning)         | ✅ |  |
 | Classification   | [ResNet50](https://github.com/Imaging-Server-Kit/extra-examples/tree/main/examples/serverkit-resnet50)         | ✅ |  |

{imaging_server_kit-0.0.12 → imaging_server_kit-0.0.14}/docs/sections/algorithm_server.md

@@ -36,20 +36,20 @@ def threshold_algo_server(image: np.ndarray, threshold: float):
 The data tuples are inspired from Napari's [LayerDataTuple](https://napari.org/0.4.15/guides/magicgui.html?highlight=layerdatatuple) model. They include three elements:
 
 - The *first element* is the **data**, usually in the form of a Numpy array. The shape and interpretation of the axes depends on what the output represents (cf. table below).
-- The *second element* is a Python dictionary representing **metadata** associated with the output. It can be empty (`{}`). These metadata are used to affect how the output is displayed in client apps (e.g. Napari).
+- The *second element* is a Python dictionary representing **metadata** associated with the output. It can be empty (`{}`). These metadata can include detection features such as *measurements* and *class labels*, and are used to affect how the output is displayed in client apps (e.g. Napari).
 - The *third element* is the output type: a string identifying what the output represents.
 
-| Output type       | Description                                                                                           |
-| ----------------- | ----------------------------------------------------------------------------------------------------- |
-| `"image"`         | An image or image-like data (incl. 3D and RGB) as a numpy array.                                         |
-| `"mask"`          | A segmentation mask (2D, 3D) as integer numpy array. Integers represent the **object class**.            |
-| `"instance_mask"` | A segmentation mask (2D, 3D) as integer nD array. Integers represent **object instances**.            |
-| `"points"`        | A collection of point coordinates (array of shape (N, 2) or (N, 3)).                                  |
-| `"boxes"`         | A collection of boxes (array of shape (N, 4, 2) representing the box corners). |
-| `"vectors"`       | Array of vectors in the Napari [Vectors](https://napari.org/stable/howtos/layers/vectors.html) format.|
-| `"tracks"`        | Array of tracks in the Napari [Tracks](https://napari.org/stable/howtos/layers/tracks.html) format.   |
-| `"class"`         | A class label (for image classification).                                                             |
-| `"text"`          | A string of text (for example, for image captioning).                                                 |
+| Output type       | Description                                                                                            |
+| ----------------- | ------------------------------------------------------------------------------------------------------ |
+| `"image"`         | An image or image-like data (incl. 3D and RGB) as a numpy array.                                       |
+| `"mask"`          | A segmentation mask (2D, 3D) as integer numpy array. Integers represent the **object class**.          |
+| `"instance_mask"` | A segmentation mask (2D, 3D) as integer nD array. Integers represent **object instances**.             |
+| `"points"`        | A collection of point coordinates (array of shape (N, 2) or (N, 3)).                                   |
+| `"boxes"`         | A collection of boxes (array of shape (N, 4, 2) representing the box corners).                         |
+| `"vectors"`       | Array of vectors in the Napari [Vectors](https://napari.org/stable/howtos/layers/vectors.html) format. |
+| `"tracks"`        | Array of tracks in the Napari [Tracks](https://napari.org/stable/howtos/layers/tracks.html) format.    |
+| `"class"`         | A class label (for image classification).                                                              |
+| `"text"`          | A string of text (for example, for image captioning).                                                  |
 
 The function can return multiple outputs, following the pattern:
 
@@ -66,6 +66,26 @@ return [
 The function parameters can only be **numpy arrays**, **numeric values** (`int`, `float`), **booleans** or **strings**.
 ```
 
+````{admonition} Handling detection features and class labels
+You can assign *measurements* and *class labels* to detected objects, such as `boxes`, `points`, or `instance_mask` types. To do this, use the `features` parameter in the output metadata. For example:
+
+```python
+boxes = (...)  # Numpy array of shape (N, 2, 2)
+probabilities = (...)  # Numpy array of shape (N,) ([0.22, 0.23, 0.65...])
+classes = (...)  # List of class labels (["elephant", "giraff", "giraff"...])
+
+boxes_params = {
+    "name": "YOLO detections",
+    "edge_color": "class",  # Optional, to parametrize object color in Napari
+    "features": {
+        "probability": probabilities,  # Detection measurements
+        "class": classes,  # Classifications must be called "class"
+    },
+}
+return [(boxes, boxes_params, "boxes")]
+```
+````
+
 ## Decorate the function with `@algorithm_server`
 
 This has several purposes:
@@ -78,13 +98,13 @@ This has several purposes:
 Below is our decorated threshold algorithm function:
 
 ```python
-from imaging_server_kit import algorithm_server, ImageUI, FloatSpinBoxUI
+from imaging_server_kit import algorithm_server, ImageUI, FloatUI
 
 @algorithm_server(
     algorithm_name="threshold",
     parameters={
         "image": ImageUI(),
-        "threshold": FloatSpinBoxUI(
+        "threshold": FloatUI(
             default=0.5,
             min=0.0,
             max=1.0,
@@ -109,21 +129,21 @@ Most importantly, we have specified the `parameters` field of `@algorithm_server
 
 The keys of the `parameters` dictionary should match the parameters of the Python function (in our example: `image` and `threshold`). The values are *parameter UI* elements. There is a UI element for each kind of parameters:
 
-| UI element           | Use case                                                                                                                         |
-| -------------------- | -------------------------------------------------------------------------------------------------------------------------------- |
-| `ImageUI`            | Input image. Validates array dimensionality (by default, accepts `2D` and `3D` arrays).                                          |
-| `MaskUI`             | Segmentation mask. Validates array dimensionality (by default, accepts `2D` and `3D` arrays).                                    |
-| `DropDownUI`         | A dropdown selector. `items` is used to specify a list of available choices.                                                     |
-| `FloatSpinBoxUI`     | Numeric parameter (floating point). Validates `min` and `max` values. `step` can be used to specify a suitable incremental step. |
-| `IntSpinBoxUI`       | Numeric parameter (integer). Validates `min` and `max` values. `step` can be used to specify a suitable incremental step.        |
-| `BoolUI`             | Boolean parameter, represented as a checkbox.                                                                                    |
-| `StringUI`           | String parameter.                                                                                                                |
-| `PointsUI`           | Points parameter.                                                                                                                |
-| `VectorsUI`          | Vectors parameter.                                                                                                               |
-| `ShapesUI`           | Shapes parameter.                                                                                                                |
-| `TracksUI`           | Tracks parameter.                                                                                                                |
-
-In our example, the input image array is well-represented by the `ImageUI` element, and the threshold parameter as a `FloatSpinBoxUI`. The parameter defaults and limits (min, max, step) are specified, as well as a title and description of the parameter, which will appear on the algorithm's `info` page.
+| UI element   | Use case                                                                                                                         |
+| ------------ | -------------------------------------------------------------------------------------------------------------------------------- |
+| `ImageUI`    | Input image. Validates array dimensionality (by default, accepts `2D` and `3D` arrays).                                          |
+| `MaskUI`     | Segmentation mask. Validates array dimensionality (by default, accepts `2D` and `3D` arrays).                                    |
+| `DropDownUI` | A dropdown selector. `items` is used to specify a list of available choices.                                                     |
+| `FloatUI`    | Numeric parameter (floating point). Validates `min` and `max` values. `step` can be used to specify a suitable incremental step. |
+| `IntUI`      | Numeric parameter (integer). Validates `min` and `max` values. `step` can be used to specify a suitable incremental step.        |
+| `BoolUI`     | Boolean parameter, represented as a checkbox.                                                                                    |
+| `StringUI`   | String parameter.                                                                                                                |
+| `PointsUI`   | Points parameter.                                                                                                                |
+| `VectorsUI`  | Vectors parameter.                                                                                                               |
+| `ShapesUI`   | Shapes parameter.                                                                                                                |
+| `TracksUI`   | Tracks parameter.                                                                                                                |
+
+In our example, the input image array is well-represented by the `ImageUI` element, and the threshold parameter as a `FloatUI`. The parameter defaults and limits (min, max, step) are specified, as well as a title and description of the parameter, which will appear on the algorithm's `info` page.
 
 Moreover, the `@algorithm_server` decorator accepts a variety of optional parameters to enable downloading a sample image, linking to a project page, and providing information on the intended usage of the algorithm server. For details, take a look at the complete [demo example](https://github.com/Imaging-Server-Kit/imaging-server-kit/blob/main/src/imaging_server_kit/demo/threshold.py). The available fields include:
 

{imaging_server_kit-0.0.12/src/imaging_server_kit/demo → imaging_server_kit-0.0.14/examples/basic}/threshold.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 import numpy as np
 import uvicorn
-from imaging_server_kit import algorithm_server, ImageUI, FloatSpinBoxUI
+from imaging_server_kit import algorithm_server, ImageUI, FloatUI
 from skimage.util import img_as_float
 
 
@@ -13,13 +13,13 @@ from skimage.util import img_as_float
     tags=["Demo"],
     parameters={
         "image": ImageUI(),
-        "threshold": FloatSpinBoxUI(
+        "threshold": FloatUI(
             default=0.5,
-            title="Threshold",
-            description="Intensity threshold.",
             min=0.0,
             max=1.0,
             step=0.1,
+            title="Threshold",
+            description="Intensity threshold.",
         ),
     },
     sample_images=[str(Path(__file__).parent / "sample_images" / "blobs.tif")],

{imaging_server_kit-0.0.12 → imaging_server_kit-0.0.14}/examples/servers/serverkit-cellpose/main.py

@@ -5,8 +5,13 @@ import numpy as np
 import uvicorn
 from cellpose import models
 
-from imaging_server_kit import (DropDownUI, FloatSpinBoxUI, ImageUI,
-                                IntSpinBoxUI, algorithm_server)
+from imaging_server_kit import (
+    DropDownUI,
+    FloatUI,
+    ImageUI,
+    IntUI,
+    algorithm_server,
+)
 
 
 @algorithm_server(
@@ -23,7 +28,7 @@ from imaging_server_kit import (DropDownUI, FloatSpinBoxUI, ImageUI,
             description="The model used for instance segmentation",
             items=["cyto", "nuclei", "cyto2"],
         ),
-        "diameter": IntSpinBoxUI(
+        "diameter": IntUI(
             default=20,
             title="Cell diameter (px)",
             description="The approximate size of the objects to detect",
@@ -31,7 +36,7 @@ from imaging_server_kit import (DropDownUI, FloatSpinBoxUI, ImageUI,
             max=100,
             step=1,
         ),
-        "flow_threshold": FloatSpinBoxUI(
+        "flow_threshold": FloatUI(
             default=0.3,
             title="Flow threshold",
             description="The flow threshold",
@@ -39,7 +44,7 @@ from imaging_server_kit import (DropDownUI, FloatSpinBoxUI, ImageUI,
             max=1.0,
             step=0.05,
         ),
-        "cellprob_threshold": FloatSpinBoxUI(
+        "cellprob_threshold": FloatUI(
             default=0.5,
             title="Probability threshold",
             description="The detection probability threshold",

{imaging_server_kit-0.0.12 → imaging_server_kit-0.0.14}/examples/servers/serverkit-orientationpy/main.py

@@ -6,9 +6,9 @@ import matplotlib
 import uvicorn
 from imaging_server_kit import (
     DropDownUI,
-    FloatSpinBoxUI,
+    FloatUI,
     ImageUI,
-    IntSpinBoxUI,
+    IntUI,
     BoolUI,
     algorithm_server,
 )
@@ -24,7 +24,7 @@ from imaging_server_kit import (
             description="The orientation computation mode.",
             items=["fiber", "membrane"],
         ),
-        "scale": FloatSpinBoxUI(
+        "scale": FloatUI(
             default=1.0,
             title="Structural scale",
             description="The scale at which orientation is computed.",
@@ -37,7 +37,7 @@ from imaging_server_kit import (
             title="Output color-coded orientation",
             description="Whether to output a color-coded representation of orientation or not.",
         ),
-        "vector_spacing": IntSpinBoxUI(
+        "vector_spacing": IntUI(
             default=3,
             title="Vector spacing",
             description="The spacing at which the orientation vectors are rendered.",

{imaging_server_kit-0.0.12 → imaging_server_kit-0.0.14}/examples/servers/serverkit-rembg/main.py

@@ -21,7 +21,7 @@ sessions: dict[str, rembg.sessions.BaseSession] = {}
             default="silueta",
             title="Model",
             description="The model used for background removal.",
-            items=["silueta", "isnet", "u2net", "u2netp", "sam"],
+            items=["silueta", "u2net"],
         ),
     },
     sample_images=[
@@ -41,42 +41,15 @@ def rembg_server(
 
     session = sessions.setdefault(rembg_model_name, rembg.new_session(rembg_model_name))
 
-    if rembg_model_name == "sam":
-        x0, y0, x1, y1 = 0, 0, image.shape[0], image.shape[1]
+    segmentation = rembg.remove(
+        data=image,
+        session=session,
+        only_mask=True,
+        post_process_mask=True,
+    )
+    segmentation = segmentation == 255
 
-        prompt = [
-            {
-                "type": "rectangle",
-                "data": [y0, x0, y1, x1],
-                "label": 2,  # `label` is irrelevant for SAM in bounding boxes mode
-            }
-        ]
-
-        segmentation = rembg.remove(
-            data=image,
-            session=session,
-            only_mask=True,
-            post_process_mask=True,
-            sam_prompt=prompt,
-        )
-        segmentation = segmentation == 0  # Invert it (for some reason)
-
-    else:
-        segmentation = rembg.remove(
-            data=image,
-            session=session,
-            only_mask=True,
-            post_process_mask=True,
-        )
-        segmentation = segmentation == 255
-
-    segmentation_params = {
-        "name": f"{rembg_model_name}_result",
-    }
-
-    return [
-        (segmentation, segmentation_params, "mask"),
-    ]
+    return [(segmentation, {"name": f"{rembg_model_name}_result"}, "mask")]
 
 
 if __name__ == "__main__":

{imaging_server_kit-0.0.12 → imaging_server_kit-0.0.14}/examples/servers/serverkit-skimage-log/main.py

@@ -8,9 +8,9 @@ from skimage.util import img_as_float
 
 from imaging_server_kit import (
     BoolUI,
-    FloatSpinBoxUI,
+    FloatUI,
     ImageUI,
-    IntSpinBoxUI,
+    IntUI,
     algorithm_server,
 )
 
@@ -19,7 +19,7 @@ from imaging_server_kit import (
     algorithm_name="skimage-LoG",
     parameters={
         "image": ImageUI(),
-        "min_sigma": FloatSpinBoxUI(
+        "min_sigma": FloatUI(
             default=5.0,
             title="Min sigma",
             description="Minimum standard deviation of the Gaussian kernel, in pixels.",
@@ -27,7 +27,7 @@ from imaging_server_kit import (
             max=100.0,
             step=0.1,
         ),
-        "max_sigma": FloatSpinBoxUI(
+        "max_sigma": FloatUI(
             default=10.0,
             title="Max sigma",
             description="Maximum standard deviation of the Gaussian kernel, in pixels.",
@@ -35,7 +35,7 @@ from imaging_server_kit import (
             max=100.0,
             step=0.1,
         ),
-        "num_sigma": IntSpinBoxUI(
+        "num_sigma": IntUI(
             default=10,
             title="Num sigma",
             description="Number of intermediate sigma values to compute between the min_sigma and max_sigma.",
@@ -43,7 +43,7 @@ from imaging_server_kit import (
             max=100,
             step=1,
         ),
-        "threshold": FloatSpinBoxUI(
+        "threshold": FloatUI(
             default=0.1,
             title="Threshold",
             description="Lower bound for scale space maxima.",
@@ -132,9 +132,7 @@ def skimage_log_server(
             (points, points_params, "points"),
         ]
     else:
-        return [
-            ("No points were detected.", {}, "text")
-        ]
+        return [("No points were detected.", {}, "text")]
 
 
 if __name__ == "__main__":

imaging_server_kit-0.0.14/examples/servers/serverkit-stackreg/README.md

@@ -0,0 +1,34 @@
+![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
+# serverkit-pystackreg
+
+Implementation of a web server for [pyStackreg](https://pystackreg.readthedocs.io/en/latest/index.html).
+
+## Installing the algorithm server with `pip`
+
+Install dependencies:
+
+```
+pip install -r requirements.txt
+```
+
+Run the server:
+
+```
+python main.py
+```
+
+The server will be running on http://localhost:8000.
+
+## Using `docker-compose`
+
+To build the docker image and run a container for the algorithm server in a single command, use:
+
+```
+docker compose up
+```
+
+The server will be running on http://localhost:8000.
+
+## Sample images provenance
+
+- pc12-unreg.tif: From the napari-pystackreg [sample image](https://github.com/glichtner/napari-pystackreg/blob/main/src/napari_pystackreg/_sample_data.py) contribution.

imaging_server_kit-0.0.14/examples/servers/serverkit-stackreg/main.py

@@ -0,0 +1,63 @@
+from typing import List
+from pathlib import Path
+import numpy as np
+import uvicorn
+from pystackreg import StackReg
+
+from imaging_server_kit import algorithm_server, ImageUI, DropDownUI, IntUI
+
+
+reg_type_dict = {
+    "affine": StackReg.AFFINE,
+    "rigid": StackReg.RIGID_BODY,
+}
+
+
+@algorithm_server(
+    title="pyStackReg",
+    description="Register one or more images to a common reference image.",
+    algorithm_name="pystackreg",
+    project_url=
+    parameters={
+        "image_stack": ImageUI(
+            title="Image stack",
+            description="2D image stack in (T)ZYX order.",
+            dimensionality=[3],
+        ),
+        "reg_type": DropDownUI(
+            title="Type",
+            description="Registration type.",
+            items=list(reg_type_dict.keys()),
+            default="rigid",
+        ),
+        "reference": DropDownUI(
+            title="Reference",
+            description="Reference for the registration",
+            items=["previous", "first", "mean"],
+            default="previous",
+        ),
+        "axis": IntUI(
+            title="Axis",
+            description="Registration axis.",
+            default=0,
+            min=0,
+            max=2,
+        ),
+    },
+    sample_images=[Path(__file__).parent / "sample_images" / "pc12-unreg.tif"],
+)
+def stackreg_server(
+    image_stack: np.ndarray,
+    reg_type: str,
+    reference: str,
+    axis: int,
+) -> List[tuple]:
+    """Run the Pystackreg algorithm."""
+    sr = StackReg(reg_type_dict.get(reg_type))
+    tmats = sr.register_stack(image_stack, reference=reference, axis=axis)
+    registered_stack = sr.transform_stack(image_stack, tmats=tmats)
+    return [(registered_stack, {"name": "Registered stack"}, "image")]
+
+
+if __name__ == "__main__":
+    uvicorn.run(stackreg_server.app, host="0.0.0.0", port=8000)

imaging_server_kit-0.0.14/examples/servers/serverkit-stackreg/requirements.txt

@@ -0,0 +1,2 @@
+imaging-server-kit
+pystackreg

imaging_server_kit-0.0.14/examples/servers/serverkit-stardist/docker-compose.yml

@@ -0,0 +1,6 @@
+services:
+  stardist:
+    build:
+      context: .
+    ports:
+      - "8000:8000"

{imaging_server_kit-0.0.12 → imaging_server_kit-0.0.14}/examples/servers/serverkit-stardist/main.py

@@ -6,8 +6,7 @@ import uvicorn
 from csbdeep.utils import normalize
 from stardist.models import StarDist2D
 
-from imaging_server_kit import (DropDownUI, FloatSpinBoxUI, ImageUI,
-                                algorithm_server)
+from imaging_server_kit import DropDownUI, FloatUI, ImageUI, algorithm_server
 
 
 @algorithm_server(
@@ -24,7 +23,7 @@ from imaging_server_kit import (DropDownUI, FloatSpinBoxUI, ImageUI,
             description="The model used for nuclei segmentation",
             items=["2D_versatile_fluo", "2D_versatile_he"],
         ),
-        "prob_thresh": FloatSpinBoxUI(
+        "prob_thresh": FloatUI(
             default=0.5,
             title="Probability threshold",
             description="Predicted object probability threshold",
@@ -32,7 +31,7 @@ from imaging_server_kit import (DropDownUI, FloatSpinBoxUI, ImageUI,
             max=1.0,
             step=0.01,
         ),
-        "nms_thresh": FloatSpinBoxUI(
+        "nms_thresh": FloatUI(
             default=0.4,
             title="Overlap threshold",
             description="Overlapping objects are considered the same when their area/surface overlap exceeds this threshold",
@@ -40,7 +39,7 @@ from imaging_server_kit import (DropDownUI, FloatSpinBoxUI, ImageUI,
             max=1.0,
             step=0.01,
         ),
-        "scale": FloatSpinBoxUI(
+        "scale": FloatUI(
             default=1.0,
             title="Scale",
             description="Scale the input image internally by this factor and rescale the output accordingly (<1 to downsample, >1 to upsample)",

imaging_server_kit-0.0.14/examples/servers/serverkit-trackpy/Dockerfile

@@ -0,0 +1,15 @@
+# Doc: https://github.com/conda-forge/miniforge-images
+FROM condaforge/miniforge3:latest
+
+ARG PYTHON_VERSION=3.10
+RUN conda install python=$PYTHON_VERSION -y
+
+WORKDIR /app
+
+COPY . .
+
+RUN python -m pip install -r requirements.txt
+
+EXPOSE 8000
+
+CMD ["python3", "main.py"]

{imaging_server_kit-0.0.12 → imaging_server_kit-0.0.14}/examples/servers/serverkit-trackpy/main.py

@@ -6,7 +6,7 @@ import pandas as pd
 import trackpy as tp
 import uvicorn
 
-from imaging_server_kit import IntSpinBoxUI, PointsUI, algorithm_server
+from imaging_server_kit import IntUI, PointsUI, algorithm_server
 
 
 @algorithm_server(
@@ -17,13 +17,13 @@ from imaging_server_kit import IntSpinBoxUI, PointsUI, algorithm_server
             description="The points to track.",
             dimensionality=[2, 3],
         ),
-        "search_range": IntSpinBoxUI(
+        "search_range": IntUI(
             default=30,
             title="Search range",
             description="Search range in pixels.",
             max=100,
         ),
-        "memory": IntSpinBoxUI(
+        "memory": IntUI(
             default=3,
             title="Memory",
             description="Maximum number of skipped frames for a single track.",

imaging_server_kit-0.0.14/examples/servers/serverkit-yolo/Dockerfile

@@ -0,0 +1,15 @@
+# Doc: https://github.com/conda-forge/miniforge-images
+FROM condaforge/miniforge3:latest
+
+ARG PYTHON_VERSION=3.10
+RUN conda install python=$PYTHON_VERSION -y
+
+WORKDIR /app
+
+COPY . .
+
+RUN python -m pip install -r requirements.txt
+
+EXPOSE 8000
+
+CMD ["python3", "main.py"]

imaging_server_kit-0.0.14/examples/servers/serverkit-yolo/README.md

@@ -0,0 +1,30 @@
+![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
+# serverkit-yolo
+
+Implementation of a web server for [YOLO](https://docs.ultralytics.com/tasks/detect/) object detection (ultralytics implementation).
+
+## Installing the algorithm server with `pip`
+
+Install dependencies:
+
+```
+pip install -r requirements.txt
+```
+
+Run the server:
+
+```
+python main.py
+```
+
+The server will be running on http://localhost:8000.
+
+## Using `docker-compose`
+
+To build the docker image and run a container for the algorithm server in a single command, use:
+
+```
+docker compose up
+```
+
+The server will be running on http://localhost:8000.

imaging_server_kit-0.0.14/examples/servers/serverkit-yolo/docker-compose.yml

@@ -0,0 +1,6 @@
+services:
+  trackpy:
+    build:
+      context: .
+    ports:
+      - "8000:8000"