%0 Journal Article %1 chen2019active %A Chen, Yuncong %A McElvain, Lauren E. %A Tolpygo, Alexander S. %A Ferrante, Daniel %A Friedman, Beth %A Mitra, Partha P. %A Karten, Harvey J. %A Freund, Yoav %A Kleinfeld, David %D 2019 %J Nature Methods %K atlasing read %N 4 %P 341--350 %R 10.1038/s41592-019-0328-8 %T An active texture-based digital atlas enables automated mapping of structures and markers across brains %U https://doi.org/10.1038/s41592-019-0328-8 %V 16 %X Brain atlases enable the mapping of labeled cells and projections from different brains onto a standard coordinate system. We address two issues in the construction and use of atlases. First, expert neuroanatomists ascertain the fine-scale pattern of brain tissue, the ‘texture’ formed by cellular organization, to define cytoarchitectural borders. We automate the processes of localizing landmark structures and alignment of brains to a reference atlas using machine learning and training data derived from expert annotations. Second, we construct an atlas that is active; that is, augmented with each use. We show that the alignment of new brains to a reference atlas can continuously refine the coordinate system and associated variance. We apply this approach to the adult murine brainstem and achieve a precise alignment of projections in cytoarchitecturally ill-defined regions across brains from different animals.

@article{chen2019active, abstract = {Brain atlases enable the mapping of labeled cells and projections from different brains onto a standard coordinate system. We address two issues in the construction and use of atlases. First, expert neuroanatomists ascertain the fine-scale pattern of brain tissue, the ‘texture’ formed by cellular organization, to define cytoarchitectural borders. We automate the processes of localizing landmark structures and alignment of brains to a reference atlas using machine learning and training data derived from expert annotations. Second, we construct an atlas that is active; that is, augmented with each use. We show that the alignment of new brains to a reference atlas can continuously refine the coordinate system and associated variance. We apply this approach to the adult murine brainstem and achieve a precise alignment of projections in cytoarchitecturally ill-defined regions across brains from different animals.}, added-at = {2019-06-12T17:45:47.000+0200}, author = {Chen, Yuncong and McElvain, Lauren E. and Tolpygo, Alexander S. and Ferrante, Daniel and Friedman, Beth and Mitra, Partha P. and Karten, Harvey J. and Freund, Yoav and Kleinfeld, David}, biburl = {https://www.bibsonomy.org/bibtex/25bbe96cf7575ad82e4971ca04ad6d6a7/dickscheid}, description = {An active texture-based digital atlas enables automated mapping of structures and markers across brains | Nature Methods}, doi = {10.1038/s41592-019-0328-8}, interhash = {5da26c6cedcfb8d14ee63977a1c6dab9}, intrahash = {5bbe96cf7575ad82e4971ca04ad6d6a7}, issn = {15487105}, journal = {Nature Methods}, keywords = {atlasing read}, number = 4, pages = {341--350}, refid = {Chen2019}, timestamp = {2019-06-12T17:45:47.000+0200}, title = {An active texture-based digital atlas enables automated mapping of structures and markers across brains}, url = {https://doi.org/10.1038/s41592-019-0328-8}, volume = 16, year = 2019 }