# 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 Cytomine app, it 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 : A execution run of an algorithm (Cytomine app) into a project. The data issued from the analysis can be retrieved from the graphical interface.

# Enable an algorithm in your project

Into 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. Add software to project

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

# 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.

Fill the form for launching job

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

The job is running


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

# Get the results

Once the job state is "Success", click on the arrow at 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 here.
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). It means you can improve it with 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 info@cytomine.com.