Run external softwares 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 jobs :

• Software : An external script using an external client (Java or Python) to make statistic computations, machine learning, image modification, etc.
• Job : A run of a software into a project. The data issued from the job can be available through the UI.

Add a software into your project

Into the Algorithms panel of the Configuration tab of a project, you can see all the softwares available.
To be able to run it, you need to activate it.

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 into the Configuration tab and activate it.

Run a job

Click on the Analysis tab and then on "Launch new analysis".
After the selection of an available algorithm, a form with all the mandatory input is displayed. Complete the form with corresponding values before running the job by clicking on "Launch new analysis".

Your job is now into the list on the below panel with its current state. The state is automatically updated.

NB : The job has the same rights than 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 software to your Cytomine instance

It is possible to add your own scripts 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 softwares available by default in a Cytomine instance are also distributed with an Open Source license. As an example, the source code of the software Segment-CV-AdaptThres-Sample is available on our GitHub repository (opens new window). It means you can improve it with push requests or by reporting issues.

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