ArticleBioinformatics (Oxford, England)2010
As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers, 1 of them a synthesis that pooled it.
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Who cites it
65 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Lineages to circuits: the developmental and evolutionary architecture of information channels into the central complex.Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology · 2023Review
- A Convenient All-Cell Optical Imaging Method Compatible with Serial SEM for Brain Mapping.Brain sciences · 2023Article
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- A scalable and modular automated pipeline for stitching of large electron microscopy datasets.eLife · 2022Article
- Fast cross-staining alignment of gigapixel whole slide images with application to prostate cancer and breast cancer analysis.Scientific reports · 2022Article
- Volume electron microscopy.Nature reviews. Methods primers · 2022Article
- Correlative Organelle Microscopy: Fluorescence Guided Volume Electron Microscopy of Intracellular Processes.Frontiers in cell and developmental biology · 2022Article
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- Elastic wrinkling of keratocyte lamellipodia driven by myosin-induced contractile stress.Biophysical journal · 2021Article
- ANHIR: Automatic Non-Rigid Histological Image Registration Challenge.IEEE transactions on medical imaging · 2020Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationTiled serial section Transmission Electron Microscopy (ssTEM) is increasingly used to describe high-resolution anatomy of large biological specimens. In particular in neurobiology, TEM is indispensable for analysis of synaptic connectivity in the brain. Registration of ssTEM image mosaics has to recover the 3D continuity and geometrical properties of the specimen in presence of various distortions that are applied to the tissue during sectioning, staining and imaging. These include staining artifacts, mechanical deformation, missing sections and the fact that structures may appear dissimilar in consecutive sections.
resultsWe developed a fully automatic, non-rigid but as-rigid-as-possible registration method for large tiled serial section microscopy stacks. We use the Scale Invariant Feature Transform (SIFT) to identify corresponding landmarks within and across sections and globally optimize the pose of all tiles in terms of least square displacement of these landmark correspondences. We evaluate the precision of the approach using an artificially generated dataset designed to mimic the properties of TEM data. We demonstrate the performance of our method by registering an ssTEM dataset of the first instar larval brain of Drosophila melanogaster consisting of 6885 images. AVAILABILITY: This method is implemented as part of the open source software TrakEM2 (http://www.ini.uzh.ch/~acardona/trakem2.html) and distributed through the Fiji project (http://pacific.mpi-cbg.de).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.