-- computational reconstruction and transformation of flattened retinae
Retistruct is an R package to morph a flat surface with cuts (a dissected flat-mount retina) onto a curvilinear surface (the a standard retinal shape). It can estimate the position of a point on the intact adult retina to within 8° of arc (3.6% of nasotemporal axis). The coordinates in reconstructed retinae can be transformed to visuotopic coordinates.
Reconstruction is achieved by: stitching the marked-up cuts of the flat-mount outline; dividing the stitched outline into a mesh whose vertices then are mapped onto a curtailed sphere; and finally moving the vertices so as to minimise a physically-inspired deformation energy function.
Retistruct has been tested on GNU/Linux (Ubuntu 12.04) and Mac OS X 10.8, and Microsoft Windows Vista. (Note that as of 30th October 2013, it is not possible to install the graphical user interface on MacOS X 10.9 (Mavericks). This is due to the RGtk2 package upon which the Retistruct GUI depends.) Instructions on how to install the latest version and use Retistruct are contained in the User Guide. The installation contains a number of demonstration retinae, and instructions for how to handle retinal flat-mount images in Retistruct.
For reference purposes, this zip file contains the review version of Retistruct and some Matlab code to read data directories contained by Retistruct.
The source code can be checked out from the R-forge subversion repository or Github.
As well as the built-in demo data, there are some sample images to practise on:
Retistruct was written by David Sterratt at the University of Edinburgh, and tested by Daniel Lyngholm and Ian Thompson at the MRC Centre for Developmental Neurobiology, KCL.
This work was supported by a Programme Grant from the Wellcome Trust (G083305).