Welcome to the tutorials for MoBIE!

The MoBIE Fiji viewer is a Fiji plugin allowing easy exploration of big multi-modal images and associated tabular data.

Main Features:

• Smooth browsing of large image data thanks to BigDataViewer
• Overlay many types of images in the same coordinate system (e.g. electron microscopy, light microscopy, segmentations…)
• Explore tabular data interactively alongside the images they’re derived from
• Easy sharing with colleagues (no need to download the raw images!)
• Easy sharing of points of interest in your data e.g. create bookmarks showing selected
• Image registration directly in MoBIE views, images and tables for your colleagues to explore
• … and more!

Get started with the tutorials below:

• Installation

Exploring existing projects

• Getting Started
• Exploring segmentations and tables
• Locations and views
• Using BigVolumeViewer
• Importing and exporting tables
• Creating your own views
• Volume Registration tutorial
• Annotation tutorial
• Grid views & image region tables
• More features

Advanced usage

• Opening projects from branches and with credentials
• Expert Mode
• Using MoBIE from the command line

Making your own projects

• MoBIE Project Creator
• Scripting Project Creation in Fiji

Data formats & MoBIE specification

• MoBIE project specification
• OME-NGFF data

High content screening

• Opening high content screening data

Use-cases and example projects

Most of the examples in the tutorial are from Whole-body integration of gene expression and single-cell morphology, where MoBIE is used to visualize a EM volume of a Platynereis dumerilii larva, derived segmentations and gene expression profiles. MoBIE supports several other data modalities and combinations thereof, for example:

• Correlative light and electron microscopy
• High-throughput microscopy
• 3D light microscopy timeseries
• Spatial transcriptomics

Live demonstrations

The MoBIE functionality is also demonstrated in a series of videos:

• MoBIE core functionality
• Creating MoBIE projects in Fiji
• Image Registration in MoBIE
• Interactive user annotation
• Timeseries in MoBIE
• Spatial Transcriptomics data in MoBIE

There is also a NEuBIAS BigData Seminar introducing MoBIE.

Citation

If you use MoBIE in your research please cite the MoBIE Nature Methods publication.

Contact

For questions or issues about MoBIE, please open a topic in the image.sc forum using the tag mobie. For specific technical issues or bugs, you can also open an issue on github.