ArticleNeuroinformatics2016
Possum-A Framework for Three-Dimensional Reconstruction of Brain Images from Serial Sections.
Article in Neuroinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Improved Post-Processing Framework for Whole Slide Imaging and 3D Reconstruction.Microscopy research and technique · 2026Article
- Imaging of developing human brains with ex vivo PSOCT and dMRI.Imaging neuroscience (Cambridge, Mass.) · 2025Article
- Molecular signatures of cortical expansion in the human foetal brain.Nature communications · 2024Article
- Molecular signatures of cortical expansion in the human fetal brain.bioRxiv : the preprint server for biology · 2024Article
- Localization and Registration of 2D Histological Mouse Brain Images in 3D Atlas Space.Neuroinformatics · 2023Article
- Review
- Refractive-index matching enhanced polarization sensitive optical coherence tomography quantification in human brain tissue.Biomedical optics express · 2022Article
- High-fidelity approximation of grid- and shell-based sampling schemes from undersampled DSI using compressed sensing: Post mortem validation.NeuroImage · 2021Article
- Diffusion MRI and anatomic tracing in the same brain reveal common failure modes of tractography.NeuroImage · 2021Article
- Insight into the fundamental trade-offs of diffusion MRI from polarization-sensitive optical coherence tomography in ex vivo human brain.NeuroImage · 2020Article
- Three-dimensional digital image construction of metaxylem vessels in root tips ofApplications in plant sciences · 2020Article
- Open access resource for cellular-resolution analyses of corticocortical connectivity in the marmoset monkey.Nature communications · 2020Article
- Article
- An active texture-based digital atlas enables automated mapping of structures and markers across brains.Nature methods · 2019Article
- A three-dimensional stereotaxic atlas of the gray short-tailed opossum (Monodelphis domestica) brain.Brain structure & function · 2018Article
- Mapping Histological Slice Sequences to the Allen Mouse Brain Atlas Without 3D Reconstruction.Frontiers in neuroinformatics · 2018Article
- Navigating the Murine Brain: Toward Best Practices for Determining and Documenting Neuroanatomical Locations in Experimental Studies.Frontiers in neuroanatomy · 2018Article
- Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template.The Journal of comparative neurology · 2016Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Techniques based on imaging serial sections of brain tissue provide insight into brain structure and function. However, to compare or combine them with results from three dimensional imaging methods, reconstruction into a volumetric form is required. Currently, there are no tools for performing such a task in a streamlined way. Here we propose the Possum volumetric reconstruction framework which provides a selection of 2D to 3D image reconstruction routines allowing one to build workflows tailored to one's specific requirements. The main components include routines for reconstruction with or without using external reference and solutions for typical issues encountered during the reconstruction process, such as propagation of the registration errors due to distorted sections. We validate the implementation using synthetic datasets and actual experimental imaging data derived from publicly available resources. We also evaluate efficiency of a subset of the algorithms implemented. The Possum framework is distributed under MIT license and it provides researchers with a possibility of building reconstruction workflows from existing components, without the need for low-level implementation. As a consequence, it also facilitates sharing and data exchange between researchers and laboratories.
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