MultiModal Big Image Data Sharing and Exploration

Explore a project

MoBIE is focused around the idea of projects - a project contains all the information needed to display your data e.g. which images and tables to display, where they are stored etc…

How to explore an existing project?

Once the MoBIE plugin has been installed (see instructions here), you can open a project:

  1. In the Fiji search bar, type: “mobie”
    …select ‘Open MoBIE Project..’ and click [ Run ]

  2. Enter the location of the project (a github repository).
    We will use the published ‘Platybrowser’ project as an example (location:

  3. The MoBIE viewer is ready to be used:

The left window contains all the controls for MoBIE, and the right is a BigDataViewer window allowing you to browse images.

Note: It is also possible to open projects from your local file system.

Browsing in the viewer

All the controls for BigDataViewer can be found under Help > Show Help in the menu at the top of the viewer.


The most important controls are:

MoBIE Controls

Each MoBIE Project is made up of a number of Datasets. Each dataset is a combination of images that can be displayed together in the same physical coordinate system. e.g. datasets could be images from different samples, timepoints, or entirely separate experiments!

In our example project, the Datasets are used to represent different versions of the data e.g. after rounds of segmentation proofreading.


Descriptions of buttons:

Sources Panel

As you add more images to the viewer, they will appear in the sources panel, like below: image

To control the image sources appearance, there are several buttons…

…and checkboxes:

Note that the available buttons and checkboxes depends on what was present in the selected view e.g. the T checkbox will only appear if a table is available.


Other Controls

There are some extra MoBIE options available by right clicking in the BigDataViewer window. For example, making high quality screenshots, or logging the current position.


See here for information about taking high quality screenshots and other features.