6 CPUs and README

.osparc/runtime.yml

@@ -11,7 +11,7 @@ settings:
     type: Resources
     value:
       Limits:
-        NanoCPUs: 8000000000 
+        NanoCPUs: 6000000000 
         MemoryBytes: 32000000000
         GenericResources:
           - DiscreteResourceSpec:

README.md

@@ -1,27 +1,61 @@
-# 
+# AxonDeepSeg GUI on o²S²PARC
 
-AxonDeepSeg in JupyterLab
+![](https://github.com/axondeepseg/axondeepseg/blob/master/docs/source/_static/logo_ads-alpha.png?raw=true)
 
-## Usage
+This repository packages AxonDeepSeg as part of a JupyterLab Service on o²S²PARC. It also adds support for pytorch+GPU/CUDA.
 
-```console
-$ make help
+AxonDeepSeg is an open-source software using deep learning and aiming at automatically segmenting axons and myelin sheaths from microscopy images. It performs 3-class semantic segmentation using a convolutional neural network. AxonDeepSeg was developed at NeuroPoly Lab, Polytechnique Montreal, University of Montreal, Canada. See [GitHub repository](https://github.com/axondeepseg/axondeepseg/) and [Documentation](https://axondeepseg.readthedocs.io/en/latest/index.html) for more information.
+
+The base of the Service was built with the [cookiecutter-osparc-ui-module](https://git.speag.com/oSparc/cookiecutter-osparc-ui-module), using [supervisord](http://supervisord.org/), [xtigervnc](https://tigervnc.org/), [novnc](https://novnc.com/info.html) and [openbox](http://openbox.org/wiki/Main_Page)
+
+## Citation
+
+If you use this work in your research, please cite:
+
+Zaimi, A., Wabartha, M., Herman, V., Antonsanti, P.-L., Perone, C. S., & Cohen-Adad, J. (2018). AxonDeepSeg: automatic axon and myelin segmentation from microscopy data using convolutional neural networks. Scientific Reports, 8(1), 3816. [Link to the paper](https://doi.org/10.1038/s41598-018-22181-4).
+
+## How to develop this o²S²PARC Service
 
+### Usage
+
+Build the module:
+```console
 $ make build
-$ make run-local
+```
+To run locally at and visit http://127.0.0.1:8888
+```console
+make run-local
+```
+To publish in local throw-away registry:
+```console
+make publish-local
+```
+
+
+### Versioning
+Service version is updated with ``make version-*``
+
+### CI/CD Integration 
+A template ci config file is created in ```.github/workflows/check-image.yml```, it checks that the image builds. When the workflow runs successfully for a new version (on the main branch), this is automatically detected and published on the internal registry (see also "Deployment on o²S²PARC" in this README)
+
+### Deployment on o²S²PARC
+
+The required CI is already packaged.
+To build and push to the internal registry you must add it to the [oSparc/docker-publisher-osparc-services](https://git.speag.com/oSparc/docker-publisher-osparc-services) repository.
 
+## How to test the Application
+Run locally and visit http://127.0.0.1:8888:
+```console
+make run-local
+```
+Or publish it in a local o²S²PARC deploy:
+```console
+make publish-local
 ```
+Perform a test segmentation as shown in this [video tutorial](https://youtu.be/zibDbpko6ko). You can use as input the image from this repository (from ```validation/inputs/input_1```) or others provided by AxonDeepSeg (e.g. [in this repository](https://github.com/axondeepseg/default-SEM-model/tree/main/model_seg_rat_axon-myelin_sem/data_test)). The input folder will be mounted in ```tmp/inputs```
+
+## Changelog
+
 
-## Workflow
-1. The [Dockerfile](jupyter-axondeepseg/src/Dockerfile) shall be modified to install additional packages and/or Jupyter kernels
-2. The [.osparc](.osparc) is the configuration folder and source of truth for metadata: describes service info and expected inputs/outputs of the service.
-3. The service docker image may be built with ``make build`` (see usage above)
-4. The service docker image may be built with ``make run-local`` (see usage above)
-5. If the image works correctly, you'll be able to access the JupyterLab interface in your browser at ``localhost:8888``
-
-## Have an issue or question?
-Please open an issue [in this repository](https://github.com/ITISFoundation/cookiecutter-osparc-service/issues/).
----
-<p align="center">
-<image src="https://github.com/ITISFoundation/osparc-simcore-python-client/blob/4e8b18494f3191d55f6692a6a605818aeeb83f95/docs/_media/mwl.png" alt="Made with love at www.z43.swiss" width="20%" />
-</p>
+### [1.0.0] - 2023-12-22
+First version