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

Opening data

• Open generic image and segmentation data
• Open various high content screening data
• Open MoBIE collection tables
• Open MoBIE projects

Advanced opening features

• Opening MoBIE projects from branches and with credentials
• Open a MoBIE project (expert mode)
• Using MoBIE from the command line

Supported file formats

Table data formats

• TSV
• Excel
• Google sheet links
• CSV
  • We recommend quoting ".." all values, because some may contain commas, which will break the format if not quoted
• Parquet

Image data formats

• Everything that Bio-Formats can open
• OME-Zarr
• BigDataViewer N5
• ilastik HDF5

Exploring image and segmentation data

• Exploring images
• Exploring segmentations and tables
• Grid views & image region tables
• Volume rendering using BigVolumeViewer
• Locations and views
• Importing and exporting tables
• Creating your own views

Conext menu items

When you right click in the BigDataViewer window there will be a context menu, including the following items:

• Select Box
• Registration - …

More documentation for the other tools will be added soon…

Image registration and annotation

• Volume registration tutorial
• Annotation tutorial
• More features

Creating a MoBIE project

Please note that creating a MoBIE project is somewhat involved. For many cases, a MoBIE collection table will do the job and is easier to create and maintain.

• Scripting Project Creation in Python
• Project Creator GUI in Fiji
• Scripting Project Creation in Fiji
• MoBIE project specification

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.