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Get Started

Get an account on a Cytomine instance


There is three main ways to get a personnal account

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



The login form

 

Your dashboard


Once logged in, you will be redirected to your dashboard. When we will have a some projects and images, your dashboard will be like ths following screenshot.
The user dashboard
It contains your recent activity, the last opened image and some statistics.

At the top of the screen, you will find the Cytomine navigation bar where the buttons will allow you to manage your projects, ontologies (these concepts will be explained further) and your uploaded images.
The Cytomine navigation bar

 

Then, you will find the quick search form allowing you to search projects and images by their name.
If you need an exhaustive listing of your search, click on the + incon to be redirected on the searching panel.

The search bar

 

At the top right of the screen, there is the account drop down menu where you will find information about your account and your activities.
The account drop down menu

 

Check your account page


On the top navigation bar, click on the Account button
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


We will upload one image of the University of Namur available through the Cytomine Open Access Collection.

Go to the Storage space to see your personal storage.
Your storage space

Into this panel, you will be able to upload your images before visualize them into Cytomine.
Once images are uploaded, you will be able to add them into a project as you will see in the next point.

 

Create a project


A project is a working space where you will put images, visualize, annotate & analyze them.

Go to Project space to see the list of the projects you are allowed to enter. 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 if you want to create a new ontology with the same name than the project, associate your project to an existing ontology or not having an associated ontology. Then, create the project by clicking on the "Save" button. You will be automatically redirected into the configuration page of the created project.

Return to the project list by clicking  the "Projects" button. You will see a new line corresponding to your project. This line can be extended to display the details of the project.
Expand the details of a project

You can now 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.
Image List1
Click on the "Add" Button for an image then close the pop-up to see the selected image displayed in the image list.
Image List2

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

 

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 your 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

 

Get back at you opened projects or images with the Workspace button


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.

 

Add 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 in this section.