Foa3D (3D Fiber Orientation Analysis) is a Python tool for multiscale nerve fiber enhancement and 3D orientation analysis in large high-resolution image volumes acquired by two-photon scanning or light-sheet fluorescence microscopy.
- parallel multiscale fiber enhancement and segmentation
- efficient multiscale fiber orientation distribution functions
- able to handle large tiled microscopy reconstructions
Please read the documentation at this page: https://lens-biophotonics.github.io/Foa3D/
Sorelli, M., Costantini, I., Bocchi, L., Axer, M., Pavone, F. S., Mazzamuto, G. (2023), Fiber enhancement and 3D orientation analysis in label-free two-photon fluorescence microscopy, Scientific Reports, 13:4160. doi: 10.1038/s41598-023-30953-w
Alimi, A., Deslauriers-Gauthier, S., Matuschke, F., Müller, A., Muenzing, S., Axer, M., & Deriche, R. (2020). Analytical and fast fiber orientation distribution reconstruction in 3D-Polarized Light Imaging. Medical Image Analysis, 65:101760. doi: 10.1016/j.media.2020.101760
Frangi, A. F., Niessen, W. J., Vincken, K. L., & Viergever, M. A. (1998). Multiscale vessel enhancement filtering. Medical Image Computing and Computer-Assisted Intervention - MICCAI'98. 1496, pp. 130-137. Springer, Berlin, Heidelberg. doi: 10.1007/BFb0056195
The research leading to the development of this open source software was conducted within the Human Brain Project, and received funding from the European Union's Horizon 2020 Framework Programme for Research and Innovation under the grant agreement No. 654148 (Laserlab-Europe) and the Specific Grant Agreements No. 785907 and No. 945539 (SGA2 and SGA3); from the General Hospital Corporation Center of the National Institutes of Health under the award number U01 MH117023; from the Italian Ministry for Education within the framework of the Euro-Bioimaging Italian Node (ESFRI research infrastructure); and from Fondazione CR Firenze (private foundation, project title: Human Brain Optical Mapping).