ArticleScientific reports2020
AMST: Alignment to Median Smoothed Template for Focused Ion Beam Scanning Electron Microscopy Image Stacks.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
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- Diel remodeling and cellular integration of the nitroplast.bioRxiv : the preprint server for biology · 2026Article
- Breeding Chlorophyll-Deficient Mutants ofBioengineering (Basel, Switzerland) · 2026Article
- CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy.Nature methods · 2025Article
- Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets.Nature protocols · 2024Review
- Differential labelling of human sub-cellular compartments with fluorescent dye esters and expansion microscopy.Nanoscale · 2023Article
- Targeted volume correlative light and electron microscopy of an environmental marine microorganism.Journal of cell science · 2023Article
- Okapi-EM: A napari plugin for processing and analyzing cryogenic serial focused ion beam/scanning electron microscopy images.Biological imaging · 2023Article
- Intracellular development and impact of a marine eukaryotic parasite on its zombified microalgal host.The ISME journal · 2022Article
- Volume electron microscopy.Nature reviews. Methods primers · 2022Article
- Identifying long-range synaptic inputs using genetically encoded labels and volume electron microscopy.Scientific reports · 2022Article
- High-precision targeting workflow for volume electron microscopy.The Journal of cell biology · 2021Article
- Cytoklepty in the plankton: A host strategy to optimize the bioenergetic machinery of endosymbiotic algae.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Review
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- Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies.Cell host & microbe · 2020Article
- Laplacian feature detection and feature alignment for multimodal ophthalmic image registration using phase correlation and Hessian affine feature space.Signal processing · 2020Article
- Two-Stage Alignment of FIB-SEM Images of Rock Samples.Journal of imaging · 2020Article
- The zebrafish as a novel model for theDisease models & mechanisms · 2020Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alignment of stacks of serial images generated by Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) is generally performed using translations only, either through slice-by-slice alignments with SIFT or alignment by template matching. However, limitations of these methods are two-fold: the introduction of a bias along the dataset in the z-direction which seriously alters the morphology of observed organelles and a missing compensation for pixel size variations inherent to the image acquisition itself. These pixel size variations result in local misalignments and jumps of a few nanometers in the image data that can compromise downstream image analysis. We introduce a novel approach which enables affine transformations to overcome local misalignments while avoiding the danger of introducing a scaling, rotation or shearing trend along the dataset. Our method first computes a template dataset with an alignment method restricted to translations only. This pre-aligned dataset is then smoothed selectively along the z-axis with a median filter, creating a template to which the raw data is aligned using affine transformations. Our method was applied to FIB-SEM datasets and showed clear improvement of the alignment along the z-axis resulting in a significantly more accurate automatic boundary segmentation using a convolutional neural network.
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Registered trials
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.