Data scientist Guide

Data are central in Cytomine.

As a data scientist, you want to be able to easily visualize data. The Cytomine graphical web interface lets you explore (whole-slide) images, annotations and any metadata associated to them. If you're not yet familiar with Cytomine, have a look at the Cytomine User Guide to have a guided tour of this graphical interface and discover the main Cytomine features.

As a data scientist, you want to be able to easily manipulate data. Here we are: all data available from the graphical interface can be manipulated programmatically from your computer.

If you don't define yourself as a data scientist but still want to manipulate Cytomine data, you're also welcome 😉 .

Create scripts

In this section, you will learn how to create scripts interacting with Cytomine, from exporting data to make statistics with your favorite library to make batch export of new images. The Interact with Cytomine page introduces the key concepts.

Create apps

Cytomine apps (also known as Cytomine software or algorithms) go one step further. It lets you create complete programs manipulating Cytomine data, run them from your computer and save results to Cytomine. Every execution is reported to Cytomine, with the parameters applied to the program. The results of each program execution can then be compared from the graphical interface. Last but not least, these apps can be plugged to Cytomine server and directly launched from the graphical interface on dedicated hardware.

If you know already how to create scripts interacting with Cytomine, read the Cytomine apps guide to discover more.