MoBIE
MultiModal Big Image Data Sharing and Exploration
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:
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
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:
More documentation for the other tools will be added soon…
Image registration and annotation
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.