Run algorithms in Cytomine

Concepts

Cytomine is useful for machine learning, data mining & image analysis by automated jobs. You will find below the list of the main concepts related to the analysis and algorithms:

• Algorithm: also known as a Cytomine app, is an external application interacting with Cytomine in a secured way and producing automated results such as statistic computations, machine learning annotations, image modification, etc.
• Analysis: is an execution of an algorithm (Cytomine app) in a project. The data from the analysis can be retrieved from the graphical interface.

Enable an algorithm in your project

In the Algorithms panel of the Configuration tab of a project, you can choose the algorithms that are enabled in your project. To be able to run an algorithm, it has to be enabled in the project.

Also, don't forget to check if the Analysis panel is displayed in the project navigation bar. If not, go to the Custom UI panel in the Configuration tab and activate it.

Launch an analysis

Click on the Analysis tab and then Launch new analysis.
After choosing an algorithm, a form with all the mandatory parameters is displayed. Complete the form with corresponding values and run the algorithm by clicking on Launch new analysis.

Your analysis is now in the list on the panel below with its current state. The state and the produced results are automatically updated.

TIP

The job has the same rights as you. If you cannot delete an image, neither can your job.

Get the results

Once the job state is Success, click on the arrow to the left of the line to get the results.

• If the job results are annotations, click on the Annotations link to be redirected on the Annotations tab where you will see all the annotations generated by this job.
• If the job results are documents, you will be able to download them.

Add your own algorithm to your Cytomine instance

It is possible to add your own algorithms as Cytomine apps to your Cytomine instance. The steps are described in the Developer Guide. You can also contact the Cytomine company to develop specific algorithms for your processes.

Licenses

All the algorithms available by default in a Cytomine instance are also distributed with an Open Source license. As an example, the source code of the Cytomine app Segment-CV-AdaptThres-Sample is available on our GitHub repository (opens new window). This means you can improve it through pull requests or by reporting issues.

If you developed some Cytomine apps and want them to be freely available to help other Cytomine users, contact uliege@cytomine.org.