Registering large volume serial-section electron microscopy image sets for neural circuit reconstruction using FFT signal whitening

Wetzel, Arthur W.; Bakal, Jeffrey A.; Dittrich, Markus; Hildebrand, David G. C.; Morgan, Josh; Lichtman, Jeff W.

doi:10.1109/aipr.2016.8010595

Cited by 29 publications

(37 citation statements)

References 27 publications

(25 reference statements)

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“…Therefore, in order to preserve the overall larval zebrafish structure and simultaneously achieve high-quality local registration, we turned to a new Signal Whitening Fourier Transform Image Registration (SWiFT-IR) method 43, 48 . Compared to conventional Pearson or phase correlation-based registration approaches, SWiFT-IR produces more robust image matching by using modulated Fourier transform amplitudes, adjusting its spatial frequency response during matching to maximize a signal-to-noise measure as its indicator of alignment quality.…”

Section: Methodsmentioning

confidence: 99%

Whole-brain serial-section electron microscopy in larval zebrafish

Hildebrand

Cicconet

Torres

et al. 2017

Nature

289

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

289

184

View full text Add to dashboard Cite

show abstract

“…In order to preserve the overall structure of the larval zebrafish and simultaneously achieve high-quality local registration, we turned to a new Signal Whitening Fourier Transform Image Registration (SWiFT-IR) method 53,57 . Compared to conventional Pearson or phase correlation-based registration approaches, SWiFT-IR produces more robust image matchings by using modulated Fourier transform amplitudes, adjusting its spatial frequency response during the image matching steps to maximize a signal-to-noise measure that serves as its main indicator of alignment quality.…”

Section: Image Alignment and Intensity Normalizationmentioning

confidence: 99%

Whole-brain serial-section electron microscopy in larval zebrafish

Hildebrand

Cicconet

Torres

et al. 2017

Preprint

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Investigating the dense meshwork of wires and synapses that form neuronal circuits is possible with the high resolution of serial-section electron microscopy (ssEM) 1 . However, the imaging scale required to comprehensively reconstruct axons and dendrites is more than 10 orders of magnitude smaller than the spatial extents occupied by networks of interconnected neurons 2 -some of which span nearly the entire brain. The difficulties in generating and handling data for relatively large volumes at nanoscale resolution has thus restricted all studies in vertebrates to neuron fragments, thereby hindering investigations of complete circuits. These efforts were transformed by recent advances in computing, sample handling, and imaging techniques 1 , but examining entire brains at high resolution remains a challenge. Here we present ssEM data for a complete 5.5 days post-fertilisation larval zebrafish brain. Our approach utilizes multiple rounds of targeted imaging at different scales to reduce acquisition time and data management. The resulting dataset can be analysed to reconstruct neuronal processes, allowing us to, for example, survey all the myelinated axons (the projectome). Further, our reconstructions enabled us to investigate the precise projections of neurons and their contralateral counterparts. In particular, we observed that myelinated axons of reticulospinal and lateral line afferent neurons exhibit remarkable bilateral symmetry. Additionally, we found that fasciculated reticulospinal axons maintain the same neighbour relations throughout the extent of their projections. Furthermore, we use the dataset to set the stage for whole-brain comparisons of structure and function by co-registering functional reference atlases and in vivo two-photon fluorescence microscopy data from the same specimen. We provide the complete dataset and reconstructions as an open-access resource for neurobiologists and others interested in the ultrastructure of the larval zebrafish.Pioneering studies in invertebrates established that synaptic-resolution wiring diagrams of complete neuronal circuits are valuable tools for relating a nervous system's structure to its function 3-6 . Such resources can be combined with perturbations, activity maps, or behavioural assays to examine how signalling through neuronal networks transforms information from the environment into relevant motor outputs 5-10 . These studies benefited from the small size of the model organisms and stereotypy across individuals, which allow for complete ssEM of an entire individual or mosaicking of data from multiple individuals.Vertebrate model nervous systems, on the other hand, are considerably larger and more variable. Consequently, ssEM of whole vertebrate neuronal circuits requires rapid computerbased technologies for acquiring, storing, and analysing many images from one animal. In many cases, anatomical data must be combined with other experiments on the same individual 11-13 to define the relationship between structure, function, and behaviour. Because verteb...

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“…First, we reduced the linear resolution of the original images by a factor five. Then we split each image into 5x5 sub-tiles and calculated the optimal alignment between each sub-tile and the corresponding sub-tile from the image above using a modified version of SWIFT-IR (Wetzel et al, 2016). Likewise, we split the regions of overlap that existing between images of the same slice into 5 sub-tiles and calculated the optimal alignment between the edges of adjacent images.…”

Section: Image Processingmentioning

confidence: 99%

Anatomy and activity patterns in a multifunctional motor neuron and its surrounding circuits

Ashaber

Tomina

Kassraian-Fard

et al. 2020

Preprint

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In most animal phyla, nerve cells form highly specific connections with each other 1,2 . The resulting intricate networks determine what activity patterns a nervous system can sustain, and hence what behaviors an animal can exhibit 3,4 . Accordingly, understanding the relationship between connectivity and activity is a major goal of neuroscience. However, despite major recent advances 5,6 , no current technology can comprehensively record activity in large nervous systems such as the human or even the mouse brain, nor can connectivity be reconstructed at synaptic level in such systems 7 . Doing both at once in the same specimen remains a distant goal.However, smaller nervous systems offer exciting opportunities today, and here we report for the first time obtaining joint functional and anatomical data from a major functional unit of the nervous system of the medicinal leech, by combining voltage-sensitive dye (VSD) 8 imaging with serial blockface electron microscopy (SBEM) 9 . We simultaneously recorded from the majority of the neurons in a segmental ganglion during several motor behaviors with a VSD sufficiently sensitive to record subthreshold neuronal activity 10,11 . We then anatomically imaged the entire ganglion with SBEM 12 . As a proof of concept, we have manually traced a critical motor neuron and identified all of its numerous presynaptic partners. The thorough reconstruction of individual synapses in combination with functional data enabled a quantitative analysis that revealed spatial clustering of synapses from functionally synchronized cell assemblies. All of our data is publicly available.

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Registering large volume serial-section electron microscopy image sets for neural circuit reconstruction using FFT signal whitening

Cited by 29 publications

References 27 publications

Whole-brain serial-section electron microscopy in larval zebrafish

Whole-brain serial-section electron microscopy in larval zebrafish

Whole-brain serial-section electron microscopy in larval zebrafish

Anatomy and activity patterns in a multifunctional motor neuron and its surrounding circuits

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