====== Introduction ======
In collaboration with [[http://neuroscience.jhu.edu/ChrisPotter.php|Chris Potter]] (when he was in [[http://www.stanford.edu/group/luolab/|Liqun Luo's lab]]) and Torsten Rohlfing (formerly Stanford, SRI, now at Google) I have developed/applied techniques for mapping different fly brains into a common frame of reference and then using this for analysing the spatial relationships between different neurons.  The software and approaches are likely to be of general relevance in neuroanatomy.

The key software component is a suite of tools ([[http://www.nitrc.org/projects/cmtk|CMTK]]) that Torsten has written for 3D image registration and analysis.  On top of this I have built a variety of data analysis tools in [[http://www.r-project.org/|R]] along with some very simple visualisation scripts in [[software:amira:start]].

====== Help ======
These wiki pages include information about many common issues using these registration approaches, but you are always welcome to contact the the [[https://www.nitrc.org/forum/forum.php?forum_id=857|CMTK user group]] (for issues with the core registration software) or the [[https://groups.google.com/forum/embed/?place=forum/nat-user|nat-user google group]] (for issues with registration GUIs or R analysis tools).

====== Published Information ======
The original [[http://www.cell.com/content/article/fulltext?uid=PIIS0092867407002048|Cell paper]] and [[http://download.cell.com/supplementarydata/cell/128/6/1187/DC1/mmc1.pdf|Supplemental Information]]

[[http://dx.doi.org/10.1016/j.cell.2007.03.006|Ann-Shyn Chiang's 2007 Cell paper]] 

[[pub:neuroanatomy:fru:start|Cachero, Ostrovsky 2010 Current Biology paper]] This page of links includes details of the analysis for our paper describing sex differences in the fly brain at the level of gross morphology and individual neuronal clusters.

[[http://dx.doi.org/10.1038/nature06808|Richard Axel's recent paper (Datta, Vasconcelos et al.)]] using a similar warping technique, including their [[http://www.nature.com/nature/journal/v452/n7186/extref/nature06808-s1.pdf|Supplemental Information]]

[[http://dx.doi.org/10.1016/j.cub.2010.11.056|Ann-Shyn Chiang's FlyCircuit paper in Current Biology]]
====== Installation ======
  * [[http://www.nitrc.org/projects/cmtk|CMTK Download]]
  * [[Registration GUI|Registration GUIs]] Original gui to use CMTK on a Mac. Also new [[http://fiji.sc|Fiji]] based cross-platform GUI.
  * [[http://flybrain.stanford.edu/R/|R analysis suite]] - A set of functions and scripts that I have written for analysing 3D images and images/tracings of neuron in R. (Original 2007 version)
    * [[https://github.com/jefferis/AnalysisSuite|latest version at github]] **Strongly Recommended** over 2007 version
  * [[Compile CMTK tools]]
 
====== How Tos ======
  * [[Registration Parameters]] (General Information)
  * [[pub:neuroanatomy:fru:registration_parameters|2010 Registration Parameters]] (Specific parameters introduced in our [[pub:neuroanatomy:fru:start|2010 Cachero, Ostrovsky et al]] paper.)
  * [[Custom command lines for munger.pl]]
  * [[Calculating an initial registration from landmarks]]
  * [[Calculating an initial surface-based registration using Amira]]
  * [[Landmarks registration in Amira]]
  * [[Landmarks registration with CMTK]]
  * [[Making Template Brains]]
  * [[Bridging different template brains]]
  * [[Test Registration Data set]] - Warpbench data set
  * [[Finding the plane of symmetry]]
  * [[Plotting 3d objects in R]]
  * [[http://www.j3d.org/matrix_faq/vectfaq_latest.html|Useful General Computational Geometry FAQ]]
  * [[Registration Quality]]
====== Notes ======
  * [[Bounding boxes and image grids]]