https://github.com/janeliascicomp/tilealignment
Alignment of the overlapping TEM images of the brain
https://github.com/janeliascicomp/tilealignment
Last synced: 12 months ago
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Alignment of the overlapping TEM images of the brain
- Host: GitHub
- URL: https://github.com/janeliascicomp/tilealignment
- Owner: JaneliaSciComp
- Created: 2016-10-17T13:14:49.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2017-03-24T17:06:28.000Z (almost 9 years ago)
- Last Synced: 2025-01-01T05:29:33.064Z (about 1 year ago)
- Language: C++
- Homepage:
- Size: 9.75 MB
- Stars: 2
- Watchers: 5
- Forks: 0
- Open Issues: 2
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Metadata Files:
- Readme: README.md
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README
Janelia Research Campus
-----------------------
Copyright (c) 2017, HHMI-Janelia Research Campus
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
* Neither the name HHMI-Janelia Research Campus nor the
names of its contributors may be used to endorse or promote products
derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL HHMI-JANELIA RESEARCH CAMPUS BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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’.