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2432 Janelia Publications

Showing 141-150 of 2432 results
07/29/23 | Network Statistics of the Whole-Brain Connectome of Drosophila
Albert Lin , Runzhe Yang , Sven Dorkenwald , Arie Matsliah , Amy R. Sterling , Philipp Schlegel , Szi-chieh Yu , Claire E. McKellar , Marta Costa , Katharina Eichler , Alexander Shakeel Bates , Nils Eckstein , Jan Funke , Gregory S.X.E. Jefferis , Mala Murthy
bioRxiv. 2023 Jul 29:. doi: 10.1101/2023.07.29.551086

Animal brains are complex organs composed of thousands of interconnected neurons. Characterizing the network properties of these brains is a requisite step towards understanding mechanisms of computation and information flow. With the completion of the Flywire project, we now have access to the connectome of a complete adult Drosophila brain, containing 130,000 neurons and millions of connections. Here, we present a statistical summary and data products of the Flywire connectome, delving into its network properties and topological features. To gain insights into local connectivity, we computed the prevalence of two- and three-node network motifs, examined their strengths and neurotransmitter compositions, and compared these topological metrics with wiring diagrams of other animals. We uncovered a population of highly connected neurons known as the “rich club” and identified subsets of neurons that may serve as integrators or broadcasters of signals. Finally, we examined subnetworks based on 78 anatomically defined brain regions. The freely available data and neuron populations presented here will serve as a foundation for models and experiments exploring the relationship between neural activity and anatomical structure.

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07/28/23 | Rastermap: a discovery method for neural population recordings
Carsen Stringer , Lin Zhong , Atika Syeda , Fengtong Du , Marius Pachitariu
bioRxiv. 2023 Jul 28:. doi: 10.1101/2023.07.25.550571

Neurophysiology has long progressed through exploratory experiments and chance discoveries. Anecdotes abound of researchers setting up experiments while listening to spikes in real time and observing a pattern of consistent firing when certain stimuli or behaviors happened. With the advent of large-scale recordings, such close observation of data has become harder because high-dimensional spaces are impenetrable to our pattern-finding intuitions. To help ourselves find patterns in neural data, our lab has been openly developing a visualization framework known as “Rastermap” over the past five years. Rastermap takes advantage of a new global optimization algorithm for sorting neural responses along a one-dimensional manifold. Displayed as a raster plot, the sorted neurons show a variety of activity patterns, which can be more easily identified and interpreted. We first benchmark Rastermap on realistic simulations with multiplexed cognitive variables. Then we demonstrate it on recordings of tens of thousands of neurons from mouse visual and sensorimotor cortex during spontaneous, stimulus-evoked and task-evoked epochs, as well as on whole-brain zebrafish recordings, widefield calcium imaging data, population recordings from rat hippocampus and artificial neural networks. Finally, we illustrate high-dimensional scenarios where Rastermap and similar algorithms cannot be used effectively.

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07/22/23 | Dissecting Cell Plate Development During Plant Cytokinesis.
Sinclair R, Cox D, Heddleston J, Aaron J, Wait E, Wilkop T, Drakakaki G
Microscopy and Microanalysis. 2023 Jul 22;29(Supplement_1):865. doi: 10.1093/micmic/ozad067.428
07/22/23 | Towards Generalizable Organelle Segmentation in Volume Electron Microscopy.
Heinrich L, Patton W, Bennett D, Ackerman D, Park G, Bogovic JA, Eckstein N, Petruncio A, Clements J, Pang S, Shan Xu C, Funke J, Korff W, Hess H, Lippincott-Schwartz J, Saalfeld S, Weigel A, CellMap Project Team
Microscopy and Microanalysis. 2023 Jul 22;29(Supplement_1):975. doi: 10.1093/micmic/ozad067.487
07/21/23 | Nonlinear manifolds underlie neural population activity during behaviour.
Fortunato C, Bennasar-Vázquez J, Park J, Chang JC, Miller LE, Dudman JT, Perich MG, Gallego JA
bioRxiv. 2023 Jul 21:. doi: 10.1101/2023.07.18.549575

There is rich variety in the activity of single neurons recorded during behaviour. Yet, these diverse single neuron responses can be well described by relatively few patterns of neural co-modulation. The study of such low-dimensional structure of neural population activity has provided important insights into how the brain generates behaviour. Virtually all of these studies have used linear dimensionality reduction techniques to estimate these population-wide co-modulation patterns, constraining them to a flat "neural manifold". Here, we hypothesised that since neurons have nonlinear responses and make thousands of distributed and recurrent connections that likely amplify such nonlinearities, neural manifolds should be intrinsically nonlinear. Combining neural population recordings from monkey motor cortex, mouse motor cortex, mouse striatum, and human motor cortex, we show that: 1) neural manifolds are intrinsically nonlinear; 2) the degree of their nonlinearity varies across architecturally distinct brain regions; and 3) manifold nonlinearity becomes more evident during complex tasks that require more varied activity patterns. Simulations using recurrent neural network models confirmed the proposed relationship between circuit connectivity and manifold nonlinearity, including the differences across architecturally distinct regions. Thus, neural manifolds underlying the generation of behaviour are inherently nonlinear, and properly accounting for such nonlinearities will be critical as neuroscientists move towards studying numerous brain regions involved in increasingly complex and naturalistic behaviours.

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07/20/23 | Toward scalable reuse of vEM data: OME-Zarr to the rescue.
Rzepka N, Bogovic JA, Moore JA
Methods in Cell Biology. 2023 Jul 20;177:359-387. doi: 10.1016/bs.mcb.2023.01.016

The growing size of EM volumes is a significant barrier to findable, accessible, interoperable, and reusable (FAIR) sharing. Storage, sharing, visualization and processing are challenging for large datasets. Here we discuss a recent development toward the standardized storage of volume electron microscopy (vEM) data which addresses many of the issues that researchers face. The OME-Zarr format splits data into more manageable, performant chunks enabling streaming-based access, and unifies important metadata such as multiresolution pyramid descriptions. The file format is designed for centralized and remote storage (e.g., cloud storage or file system) and is therefore ideal for sharing large data. By coalescing on a common, community-wide format, these benefits will expand as ever more data is made available to the scientific community.

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07/15/23 | Pinpoint: trajectory planning for multi-probe electrophysiology and injections in an interactive web-based 3D environment
Daniel Birman , Kenneth J. Yang , Steven J. West , Bill Karsh , Yoni Browning , the International Brain Laboratory , Joshua H. Siegle , Nicholas A. Steinmetz
bioRxiv. 2023 Jul 15:. doi: 10.1101/2023.07.14.548952

Targeting deep brain structures during electrophysiology and injections requires intensive training and expertise. Even with experience, researchers often can't be certain that a probe is placed precisely in a target location and this complexity scales with the number of simultaneous probes used in an experiment. Here, we present Pinpoint, open-source software that allows for interactive exploration of stereotaxic insertion plans. Once an insertion plan is created, Pinpoint allows users to save these online and share them with collaborators. 3D modeling tools allow users to explore their insertions alongside rig and implant hardware and ensure plans are physically possible. Probes in Pinpoint can be linked to electronic micro-manipulators allowing real-time visualization of current brain region targets alongside neural data. In addition, Pinpoint can control manipulators to automate and parallelize the insertion process. Compared to previously available software, Pinpoint's easy access through web browsers, extensive features, and real-time experiment integration enable more efficient and reproducible recordings.

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07/13/23 | Localization of fixed dipoles at high precision by accounting for sample drift during illumination
Hinterer F, Schneider MC, Hubmer S, López-Martínez M, Ramlau R, Schütz GJ
Applied Physics Letters. 2023 Jul 13;123(2):. doi: 10.1063/5.0137834

Single molecule localization microscopy relies on the precise quantification of the position of single dye emitters in a sample. This precision is improved by the number of photons that can be detected from each molecule. Particularly recording at cryogenic temperatures dramatically reduces photobleaching and would, hence, in principle, allow the user to massively increase the illumination time to several seconds. The downside of long illuminations, however, would be image blur due to inevitable jitter or drift occurring during the illuminations, which deteriorates the localization precision. In this paper, we theoretically demonstrate that a parallel recording of the fiducial marker beads together with a fitting approach accounting for the full drift trajectory allows for largely eliminating drift effects for drift magnitudes of several hundred nanometers per frame. We showcase the method for linear and diffusional drift as well as oscillations, assuming fixed dipole orientations during each illumination.

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07/10/23 | Input density tunes Kenyon cell sensory responses in the Drosophila mushroom body.
Ahmed M, Rajagopalan AE, Pan Y, Li Y, Williams DL, Pedersen EA, Thakral M, Previero A, Close KC, Christoforou CP, Cai D, Turner GC, Clowney EJ
Current Biology. 2023 Jul 10;33(13):2742-2760.e12. doi: 10.1016/j.cub.2023.05.064

The ability to discriminate sensory stimuli with overlapping features is thought to arise in brain structures called expansion layers, where neurons carrying information about sensory features make combinatorial connections onto a much larger set of cells. For 50 years, expansion coding has been a prime topic of theoretical neuroscience, which seeks to explain how quantitative parameters of the expansion circuit influence sensory sensitivity, discrimination, and generalization. Here, we investigate the developmental events that produce the quantitative parameters of the arthropod expansion layer, called the mushroom body. Using Drosophila melanogaster as a model, we employ genetic and chemical tools to engineer changes to circuit development. These allow us to produce living animals with hypothesis-driven variations on natural expansion layer wiring parameters. We then test the functional and behavioral consequences. By altering the number of expansion layer neurons (Kenyon cells) and their dendritic complexity, we find that input density, but not cell number, tunes neuronal odor selectivity. Simple odor discrimination behavior is maintained when the Kenyon cell number is reduced and augmented by Kenyon cell number expansion. Animals with increased input density to each Kenyon cell show increased overlap in Kenyon cell odor responses and become worse at odor discrimination tasks.

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07/07/23 | Volume electron microscopy.
Peddie CJ, Genoud C, Kreshuk A, Meechan K, Micheva KD, Narayan K, Pape C, Parton RG, Schieber NL, Schwab Y, Titze B, Verkade P, Aubrey A, Collinson LM
Nature Reviews: Methods Primers. 2022 Jul 07;2:51. doi: 10.1038/s43586-022-00131-9

Life exists in three dimensions, but until the turn of the century most electron microscopy methods provided only 2D image data. Recently, electron microscopy techniques capable of delving deep into the structure of cells and tissues have emerged, collectively called volume electron microscopy (vEM). Developments in vEM have been dubbed a quiet revolution as the field evolved from established transmission and scanning electron microscopy techniques, so early publications largely focused on the bioscience applications rather than the underlying technological breakthroughs. However, with an explosion in the uptake of vEM across the biosciences and fast-paced advances in volume, resolution, throughput and ease of use, it is timely to introduce the field to new audiences. In this Primer, we introduce the different vEM imaging modalities, the specialized sample processing and image analysis pipelines that accompany each modality and the types of information revealed in the data. We showcase key applications in the biosciences where vEM has helped make breakthrough discoveries and consider limitations and future directions. We aim to show new users how vEM can support discovery science in their own research fields and inspire broader uptake of the technology, finally allowing its full adoption into mainstream biological imaging.

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