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Contributor: Gennady Denisov
Acknowledgements: Khaled Khairy and Goran Ceric
This repository stores two codes for alignment of tiles produced by the FlyTEM project at Janelia. The project is aimed at imaging and assembly of the entire CNS of fruit flies, and providing software tools to extract skeletons of neuroanatomical structures of these species.
The first code performs a pairwise alignment of a couple of adjacent tiles and reports the point matches between the two. This software makes use of a modified portion of the code borrowed from another repository, https://github.com/billkarsh/Alignment_Projects, primarily from the folder 1_DMesh, together with a re-designed interface. The alignment is performed using an executable ‘align2’ thus produced. The detailed instruction and an example of usage for this executable can be found in ‘docs/README_pairwise’.
The second code is aimed at a multiple tile alignment. The point matches between couples of tiles generated by align2, or by another similar tool, can be used to formulate the problem of a direct simultaneous alignment of a large number (say, thousands or millions) of tiles. Mathematically, this problem reduces to solving a very large sparse system of linear algebraic equations. In fact, the second code serves as an adapter for solving this sparse system using the linear solver PaStiX (http://pastix.gforge.inria.fr). A detailed instruction for compiling and using this code can be found in ‘docs/README_multi’.
To compile all the code in this repository, type ‘make’. The commands to compile separately the pairwise or multiple alignment code are ‘make align2’ and ‘make align_multi’, respectively. The compiled executables, together with utility scripts, will be stored in the folder ‘bin’.