{"id":18964142,"url":"https://github.com/janeliascicomp/tilealignment","last_synced_at":"2026-04-02T19:30:21.160Z","repository":{"id":93115042,"uuid":"71140266","full_name":"JaneliaSciComp/TileAlignment","owner":"JaneliaSciComp","description":"Alignment of the overlapping TEM images of the brain","archived":false,"fork":false,"pushed_at":"2017-03-24T17:06:28.000Z","size":10219,"stargazers_count":2,"open_issues_count":2,"forks_count":0,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-01-01T05:29:33.064Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/JaneliaSciComp.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-10-17T13:14:49.000Z","updated_at":"2019-04-10T15:03:26.000Z","dependencies_parsed_at":"2023-03-06T19:01:20.119Z","dependency_job_id":null,"html_url":"https://github.com/JaneliaSciComp/TileAlignment","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2FTileAlignment","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2FTileAlignment/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2FTileAlignment/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2FTileAlignment/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JaneliaSciComp","download_url":"https://codeload.github.com/JaneliaSciComp/TileAlignment/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239959947,"owners_count":19725221,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-08T14:23:03.133Z","updated_at":"2026-04-02T19:30:21.037Z","avatar_url":"https://github.com/JaneliaSciComp.png","language":"C++","readme":"Janelia Research Campus\r\n-----------------------\r\n\r\n![jrc_logo_180x40](https://cloud.githubusercontent.com/assets/1093770/23528799/206de32e-ff69-11e6-9fac-38bac908aed1.png)\r\n\r\nCopyright (c) 2017, HHMI-Janelia Research Campus\r\nAll rights reserved.\r\n\r\nRedistribution and use in source and binary forms, with or without\r\nmodification, are permitted provided that the following conditions are met:\r\n\r\n    * Redistributions of source code must retain the above copyright\r\n      notice, this list of conditions and the following disclaimer.\r\n      \r\n    * Redistributions in binary form must reproduce the above copyright\r\n      notice, this list of conditions and the following disclaimer in the\r\n      documentation and/or other materials provided with the distribution.\r\n      \r\n    * Neither the name HHMI-Janelia Research Campus nor the\r\n      names of its contributors may be used to endorse or promote products\r\n      derived from this software without specific prior written permission.\r\n\r\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND\r\nANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED\r\nWARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\r\nDISCLAIMED. IN NO EVENT SHALL HHMI-JANELIA RESEARCH CAMPUS BE LIABLE FOR ANY\r\nDIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES\r\n(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;\r\nLOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND\r\nON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT\r\n(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS\r\nSOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\r\n\r\n\r\nContributor: Gennady Denisov\r\n\r\nAcknowledgements: Khaled Khairy and Goran Ceric \r\n\r\nThis 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.\r\n\r\nThe 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’. \r\n\r\nThe 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’. \r\n\r\nTo 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’.\r\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjaneliascicomp%2Ftilealignment","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjaneliascicomp%2Ftilealignment","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjaneliascicomp%2Ftilealignment/lists"}