# Getting started

# Get an account

There are three main ways to get a personal account:

When you have a username and a password, go to the login page and ... Welcome into Cytomine !

The login page

# Your dashboard

Once logged in, you are redirected to your dashboard. It contains your recent activity, the last opened image and some statistics. If it is the first time you log in to Cytomine, it is quite empty as you don't have any activity yet. When we will have a some projects and images, your dashboard will be like the following screenshot.

The user dashboard

At the top of the screen, there is the Cytomine navigation bar to access different spaces in order to manage your projects, ontologies and your uploaded images. These concepts will be further detailed in this guide.

The Cytomine navigation bar

At right, the quick search form allows you to search projects and images by their name. If you need an exhaustive listing of your search, click on the + icon to be redirected on the advanced search panel.

The search bar

Next to the quick search bar, at the top right of the screen, the account drop down menu (displayed with your name) lets you find information about your personal account and your activity on Cytomine.

The account drop down menu

# Your account page

In the account drop down menu in the top navigation bar, click on Account

Account button

and change your password.

Password panel

You will see some connexion keys. They will be explained in the Data Science part of this documentation.

# Upload an image

In this guide, we will upload one image of the University of Namur (opens new window) available through the Cytomine Open Access Collection (opens new window) as an example.

Go to the Storage space to see your personal storage.

Your storage space

It is the right place to upload your images before visualize them into Cytomine.

Add one or several images at once with the green Add Files button. Then, click on Start upload to launch the import of your images to Cytomine. Once images are fully imported, they will appear in the Storage panel. These images are ready to be added to a project in order to visualize them, as we will see in the next steps of this guide.

# Create a project

A project is a working space where to organize, visualize, annotate and analyze images. This working space can also be shared between multiple Cytomine users.

Go to Project space to see the list of the projects you have access to. Each line corresponds to a specific project.

Your project list

To create a new project, click on the New Project button. A pop-up is displayed.

Your project creation pop-up

Give a name to your project, then choose the project ontology. You can

  1. do not use any ontology for your new project,
  2. associate this new project to an existing ontology,
  3. create a new ontology with the same name as this new project.

In this Getting Started guide, we will use the third option.

Then, create the project by clicking on the Save button. You are automatically redirected to the configuration page of this just created project. At this stage, we will keep the default project configuration.

Return to the project list by clicking on Projects in the Cytomine navigation bar. There is a new line corresponding to your new project. This line can be extended to display the details of the project.

Expand the details of a project.

You can enter into your new project by clicking on the project name or on the Open button.

# Add images

To be able to interact with the images, we need to associate them with our current project. Go to the images panel and click on the "Add image" button. You will see a list with all your previously uploaded images.

Click on the "Add" Button for an image then close the pop-up to see the selected image displayed in the image list.

As in the project list, you can expand a line to display some details about the image (resolution, size, vendor).

# Browse an image

Into these list of the associated images into this project. Click on the Open button to browse the image.

Browsing through the selected image

Use the +/- buttons or your mouse wheel to zoom into your image and the left click to drag for browsing into the image. On the right panel, you will find a menu related to your exploration : you can see the layer of other users and properties associated to annotations, change the color balance of the image, etc. But currently, there is no annotation on this image. We will add them in the next point.

# Add annotations

On the top navigation bar into the browsing view, you can select a mode for adding annotation. To draw a circle annotation, click on "Circle" then put your mouse on a zone of the image, click at the wanted center position of the annotation and move your mouse to determine the radius. A lot of geometric forms are possible and also a free draw tool.

Once the annotation is created, you will see a infobox that will allow you to get the annotation size, add description, terms, tags, properties and so on.

Draw an annotation using the free draw tool

# Add terms to ontology

The main interest of annotations are the terms than we can associate with them to classify annotations and analyze images. Go to the project dashboard and click on the Ontology link. On this space, you are able to add term and the associated color to your ontology.

Term add to the ontology

# Your Workspace

In the top navigation bar, the Workspace drop down menu will list all the currently opened projects and images during this session and allow you to return quickly in these projects or images.

The workspace drop down menu

If you followed this page, you have the project test with the previously opened image into this list.

Now, return to the previously opened image by clicking on the "Workspace" button and clicking on the image's name.

# Associate terms to your annotation

Click on the Select button in the annotation bar to select your previously drawned annotation and you can now associated terms to your annotation. The annotation have now a color.

Term add to my annotation

You can continue to draw annotation and associate the good terms on your annotations.

# Configure your project

Until now, we have used the default configuration of our project but you can custom the access, the displayed panel and so on. Go to the Configuration panel to be able to set the UI access for your contributors (users into your project) and managers (administrators of your project), the software associated with this project, the image filters, the global permissions (Read Only, Restricted or Classic project).

Custom the UI of a project

As an example, in the Custom UI panel, we will be able to disable some annotation tools : the Elipse will be not used at all and the other geometric forms must not be used by my contributors (but the managers will still be able to use it).

# Add other users

To plainfully use the collaborative aspects of Cytomine, you need to add other users into your project. Go to the Configuration tab and add a new contributor by clicking on the "Add members" button. You are now able to see the layer of its new user into an image and see its annotations.

Add a new contributors

If you want to promote a contributor as manager, you can click on the human icon in the "Role" column to modify its permissions into the project.

# What to do next

You will find more information about the exposed concepts in the other pages of this section. If you are not familiar with Cytomine, let's begin with Project