Robust registration of calcium images by learned contrast synthesis

Bogovic, John A.; Hanslovsky, Philipp; Wong, Allan; Saalfeld, Stephan

doi:10.1109/isbi.2016.7493463

Cited by 153 publications

(135 citation statements)

References 14 publications

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“…Correspondence of individual neurons or functional reference atlas regions across imaging modalities was achieved with landmark-based 3-D thin-plate spline warping of each fluorescence dataset to the ssEM dataset using BigWarp 49 .…”

Section: Methodsmentioning

confidence: 99%

Whole-brain serial-section electron microscopy in larval zebrafish

Hildebrand

Cicconet

Torres

et al. 2017

Nature

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317

184

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High-resolution serial-section electron microscopy (ssEM) makes it possible to investigate the dense meshwork of axons, dendrites, and synapses that form neuronal circuits(1). However, the imaging scale required to comprehensively reconstruct these structures is more than ten orders of magnitude smaller than the spatial extents occupied by networks of interconnected neurons(2), some of which span nearly the entire brain. Difficulties in generating and handling data for large volumes at nanoscale resolution have thus restricted vertebrate studies to fragments of circuits. These efforts were recently transformed by advances in computing, sample handling, and imaging techniques(1), but high-resolution examination of entire brains remains a challenge. Here, we present ssEM data for the complete brain of a larval zebrafish (Danio rerio) at 5.5 days post-fertilization. Our approach utilizes multiple rounds of targeted imaging at different scales to reduce acquisition time and data management requirements. The resulting dataset can be analysed to reconstruct neuronal processes, permitting us to survey all myelinated axons (the projectome). These reconstructions enable precise investigations of neuronal morphology, which reveal remarkable bilateral symmetry in myelinated reticulospinal and lateral line afferent axons. We further set the stage for whole-brain structure-function comparisons by co-registering functional reference atlases and in vivo two-photon fluorescence microscopy data from the same specimen. All obtained images and reconstructions are provided as an open-access resource

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Section: Methodsmentioning

confidence: 99%

Whole-brain serial-section electron microscopy in larval zebrafish

Hildebrand

Cicconet

Torres

et al. 2017

Nature

Self Cite

317

184

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“…In addition, eYFP fluorescence from ChR2-EYFP contributes to the v3D signal ( Figure 4A). We therefore used a semi-manual landmark-based method to align brain volumes (Bogovic et al, 2016). Point correspondences between the v3D and AAT were manually determined.…”

Section: Three-dimensional Templatesmentioning

confidence: 99%

“…We used a landmark-based registration package (BigWarp in ImageJ (Bogovic et al, 2016)) in which corresponding landmarks can be identified in two image stacks. The warping algorithm uses a thin plate spline for interpolation between landmarks (Duchon, 1977).…”

Section: Brain Registrationmentioning

confidence: 99%

Accurate localization of linear probe electrodes across multiple brains

Liu

Chen

Economo

et al. 2020

Preprint

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Recently developed silicon probes have large numbers of recording electrodes on long linear shanks. Specifically, Neuropixels probes have 960 recording electrodes distributed over 9.6 mm shanks. Because of their length, Neuropixels probe recordings in rodents naturally span multiple brain areas. Typical studies collate recordings across several recording sessions and animals. Neurons recorded in different sessions and animals have to be aligned to each other and to a standardized brain coordinate system. Here we report a workflow for accurate localization of individual electrodes in standardized coordinates and aligned across individual brains. This workflow relies on imaging brains with fluorescent probe tracks and warping 3-dimensional image stacks to standardized brain atlases. Electrophysiological features are then used to anchor particular electrodes along the reconstructed tracks to specific locations in the brain atlas and therefore to specific brain structures. We performed ground-truth experiments, in which motor cortex outputs are labelled with ChR2 and a fluorescence protein. Recording from brain regions targeted by these outputs reveals better than 100 µm accuracy for electrode localization.

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“…Software solutions are being developed, in the form of software that aids visualisation and alignment of large 3D image data, including the FIJI plugins TrakEM2 [49], BigDataViewer [50] and BigWarp [51], and ec-CLEM [52] on the ICY platform. These algorithms depend on manual identification of matching landmarks within the datasets for alignment, and can only work to an accuracy that is determined by the extent of the sample distortions caused by intermediate sample preparation steps.…”

Section: Correlative Microscopy Of Volumesmentioning

confidence: 99%