ArticlePloS one2019
Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 105 papers, 1 of them a synthesis that pooled it.
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Who cites it
105 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Deep Learning Based Cross-Modality Histological Brain Section Registration in Multiple Species Using Synthetic Images.bioRxiv : the preprint server for biology · 2026Article
- Efferent projections of topographically distinct relaxin family peptide receptor-3 (RXFP3) lateral hypothalamus/zona incerta cells.Brain structure & function · 2026Article
- Opioid- and NMDA-receptor-dependent neural plasticity mediates long-term analgesia from motor cortical stimulation.bioRxiv : the preprint server for biology · 2026Article
- A brainstem pathway underlying vagal modulation of somatic pain and affective states.Nature neuroscience · 2026Article
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- Logistic regression for estimating functional effects with spatial transcriptomics.Nucleic acids research · 2026Article
- Lipofuscin accumulation in aging and CLN1 is associated with deficient de-S-acylation, lyso-mitochondrial dysfunction, and lipid dyshomeostasis.Acta neuropathologica · 2026Article
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- SCALPEL: A pipeline for processing large-scale spatial transcriptomics data.bioRxiv : the preprint server for biology · 2026Article
- Deficient de-S-acylation in aging and CLN1 contributes to lyso-mitochondrial dysfunction, lipid dyshomeostasis, and resultant lipofuscin biogenesis.Research square · 2026Article
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- Exercise evokes retained motor performance without neuroprotection in a mouse model of Parkinson's disease.Frontiers in physiology · 2026Article
45 more citing papers are in PubMed but not listed here.
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Modern high throughput brain wide profiling techniques for cells and their morphology, connectivity, and other properties, make the use of reference atlases with 3D coordinate frameworks essential. However, anatomical location of observations made in microscopic sectional images from rodent brains is typically determined by comparison with 2D anatomical reference atlases. A major challenge in this regard is that microscopic sections often are cut with orientations deviating from the standard planes used in the reference atlases, resulting in inaccuracies and a need for tedious correction steps. Overall, efficient tools for registration of large series of section images to reference atlases are currently not widely available. Here we present QuickNII, a stand-alone software tool for semi-automated affine spatial registration of sectional image data to a 3D reference atlas coordinate framework. A key feature in the tool is the capability to generate user defined cut planes through the reference atlas, matching the orientation of the cut plane of the sectional image data. The reference atlas is transformed to match anatomical landmarks in the corresponding experimental images. In this way, the spatial relationship between experimental image and atlas is defined, without introducing distortions in the original experimental images. Following anchoring of a limited number of sections containing key landmarks, transformations are propagated across the entire series of sectional images to reduce the amount of manual steps required. By having coordinates assigned to the experimental images, further analysis of the distribution of features extracted from the images is greatly facilitated.
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