- Tissue Tagging for ultra-fast staining of thick, fixed tissue
- NBLAST neuron search and similarity
- Bridging Registrations can be used to integrate data registered against different template brains. We also provide a large amount of bridged data for download. The easiest way to get this is to go to the virtualflybrain.org image downloads page.
- We contribute to the Virtual Fly Brain site of which Greg is a PI since Oct 2014.
- Key Jefferis Lab R packages includes detailed documentation
- Jefferis lab github
- Greg’s github all lab code is available from one of these two github sites.
We have expended a lot of effort in developing tools for image analysis and related problems in our work. We have benefitted greatly from open source tools and all of our software is developed open source and available via the github repositories listed above or through large public projects to which we have made contributions such as ImageJ/Fiji and the CMTK registration suite.
We have also made somewhat more specialist toolsets for working with neuroanatomical data. This includes our neuroanatomy toolbox (nat) suite of software, developed as fully documented and tested packages for the R statistical environment and available both at github and CRAN (The Comprehensive R Archive Network). We also provide documented examples of using nat for analysing neuroanatomical data from a variety of model systems in the nat.examples repository.