Application details for the OpenScope program – a platform for high-throughput and reproducible neurophysiology.

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This dataset was collected for the Global Local Oddball project, as part of the OpenScope project.

This dataset was collected for the Illusion project, as part of the OpenScope project.

This dataset was collected for the Dendritic Coupling project, as part of the OpenScope project.

This dataset was collected for the Credit Assignment project, as part of the OpenScope project.

This dataset was collected for the Predictive Coding project, as part of the OpenScope project.

This study investigates the effects of periodic sensory stimulation (PSS) on the activity of neurons of different types in the mouse visual cortex.

We used two-photon calcium imaging in mice of both sexes to systematically survey stimulus-evoked neurophysiological differentiation (ND) in excitatory neuronal populations in layers (L)2/3, L4, and L5 across five visual cortical areas (primary, lateromedial, anterolateral, posteromedial, and anteromedial) in response to naturalistic and phase-scrambled movie stimuli.

The OpenScope program publishes on an annual basis a detailed public report that summarizes all of our activities within the year. These reports highlight all developments of the year: new selected projects, completed projects, publications and technical developments of the platform.

The OpenScope program publishes on an annual basis a detailed public report that summarizes all of our activities within the year. These reports highlight all developments of the year: new selected projects, completed projects, publications and technical developments of the platform.

The OpenScope program publishes on an annual basis a detailed public report that summarizes all of our activities within the year. These reports highlight all developments of the year: new selected projects, completed projects, publications and technical developments of the platform.

A library that defines AIND data schema and validates JSON.

The multiplane pipeline processes planar optical physiology data acquired in parallel to extract events from the ROIs in each plane.

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The ExA-SPIM method represents a major breakthrough in microscopy. Schneider-Kreuznach's DIAMOND lenses play a crucial role. Their large image circle and high magnification allow the analysis of larger samples in a single image without additional segmentation.

Repository that hosts the SmartSPIM pipeline code.

A Harp-compatible device for controlling an instrumented mouse treadmill.

Signal conditioning board for an implanted thermistor.

An ephys-compliant capacitive lick detector.

A Harp core implementation on the RP2040

This webpage stores metadata, experimental details and project description associated and ran by the OpenScope program. OpenScope is a platform for high-throughput and reproducible neurophysiology open to external scientists to test theories of brain function.

We developed a silicon probe for extracellular electrophysiology which samples neuronal activity at ultra-high spatial density, allowing us to more accurately and sensitively measure neural activity.

We characterize the impact of stimulus novelty on disinhibitory circuit components using longitudinal 2-photon calcium imaging of Vip, Sst, and excitatory populations in the mouse visual cortex.

We describe a novel 3D-printed cranial-replacement implant (SHIELD) enabling electrophysiological recordings from distributed areas of the mouse brain, which allows us to measure spiking dynamics across many interacting brain regions.

We present a large-scale analysis of saccadic behaviors in head-fixed mice and their neural correlates. We find that saccade-responsive neurons are present across visual cortex, but their distribution varies considerably by transgenically defined cell type, cortical area, and cortical layer.

Using cellular resolution, mesoscale two-photon calcium imaging and multi-Neuropixels recordings in the mouse visual cortex, we identified a sparse subset of neurons in the primary visual cortex (V1) and higher visual areas that respond emergently to illusory contours, which are key tools to study sensory inference.

To address the question of how factors' (such as brain states and behaviors) relative impact neuronal variability evolves over time, we designed an encoding model with latent states to partition visual cortical variability across three crucial categories of sources: internal brain dynamics, behavior, and external visual stimulus.

We employed a large-scale public 16 dataset of electrophysiological recordings in the visual cortex of awake, behaving mice using 17 Neuropixels probes and designed population network models to investigate the observed 18 changes in neural dynamics in response to a combination of distinct forms of novelty.

We investigate the question of how distinct animal reward strategies differentially engage brain circuits, focusing on the cortical Vip-Sst disinhibitory circuit between vasoactive intestinal peptide-postive (Vip) interneurons and somatostatin-positive (Sst) interneurons.

We establish a set of benchmarks for comparing the performance of various compression algorithms on experimental and simulated recordings from Neuropixels 1.0 (NP1) and 2.0 (NP2) probes.

We present a new expansion-assisted selective plane illumination microscope, which, combined with new tissue clearing and expansion methods, the microscope allows imaging centimeter-scale samples with 250×250×750 nm optical resolution (4× expansion), including entire mouse brains, with high contrast and without sectioning.

The SmartSPIM is an axially swept lightsheet microscope that produces uniform axial resolution across the entire imaging volume of large biological samples, such as whole mouse brains.

This protocol provides instructions to prepare the SmartSPIM microscope, to load samples, and to acquire data.

This protocol details the steps for staining 4% PFA fixed mouse brain tissue sections with DAPI (4',6-diamidino-2-phenylindole), a fluorescent stain that can be used to label anatomic regions of interest in a mouse brain, allowing for imaging with a fluorescent microscope.

The Immunohistochemistry (IHC) Staining for Mouse Brain Sections protocol details the blocking, primary, and secondary antibody staining of 50-100 micron mouse brain tissue slices fixed in 4% PFA.

This protocol details mounting thin sliced mouse brain tissue sections onto charged slides in a uniform orientation that does not create wrinkles or artifacts that might interfere with imaging, and then how to apply a coverslip.

This is a protocol that details sectioning a mouse brain fixed in 4% PFA and 30% sucrose on a sliding microtome.

This protocol collection details the steps for a whole mouse brain specimen to be perfused, sliced, stained with antibodies, DAPI, or both, and made into slides.

This protocol describes the process of coating an implant with duragel in preparation for in vivo electrophysiology experiments.

This protocol describes the procedure for removing the SORTA-clear plug used in acute in vivo electrophysiology experiments in whole-hemisphere craniotomy (WHC) preparation mice with Neuropixels probes.

This protocol describes the procedure for making agarose used in acute in vivo Electrophysiology Experiments with Neuropixels probes.

This protocol describes a customized mouse habituation protocol for mice within experiments involving head fixation onto disks.

This protocol describes a semi-customized workflow to perform water restriction with mice designated for future experiments.

This protocol describes the pre-operative setup and post-operative take-down procedures utilized for rodent stereotaxic neurosurgical procedures.

This protocol describes the steps necessary to apply this silicone layer in advance of a cranial windowing procedure.

This protocol describes the delipidation of a mouse brain specimen using a modified iDISCO protocol.

When paired with organic delipidation, these steps can return a solvent-shrunken brain to normal size in phosphate buffer, suitable for post-delipidation antibody labeling.

This protocol produces a delipidated whole brain that can be further processed for expansion or index-matched for immediate imaging.

To amplify signals of FPs for high resolution, multi-scale imaging, we immunolabel delipidated brain samples.

We have imaged expanded whole mouse brains generated using this protocol on our custom built ExA-SPIM microscope without need for any tissue slicing. These whole brain data sets are being used for tracing complete axonal morphology of individual neurons.

We generated variants of the fluorescent glutamate indicator iGluSnFR with improved signal-to-noise ratios and kinetics, to enable better imaging of neurotransmission with genetic and molecular specificity.

The Kaspar Podgorski Lab has deposited materials at Addgene for distribution to the research community. We are developing fluorescent indicators that report subthreshold inputs to directly read out intricate three-dimensional patterns of synaptic activity in behaving animals, so that we can infer how neurons transform inputs into outputs.

The SLAP2 is a revolutionary new microscope based on a technological breakthrough called second-generation Scanned Line Angular Projection two photon laser scanning microscopy that was recently developed by Dr. Kaspar Podgorski at the Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA.

HortaCloud is a streaming 3D annotation platform for large microscopy data that runs entirely in the cloud. It is a free, open source research software tool, developed by Janelia Research Campus. The Allen Institute uses HortaCloud to proofread whole-brain images of neurons collected on various fluorescence microscopy instruments.

Set of tools that work with and enhance the Google neuroglancer tool for volume visualization and annotation.

With funding from the National Institutes of Health (NIH) and technology from Amazon Web Services (AWS), the Allen Institute is leading an effort to build the Brain Knowledge Platform (BKP) – soon to be the largest open-source database of brain cell data in the world. The BKP will host the ABC Atlas including single-cell resolution neuroscience datasets from collaborative teams worldwide. It will be the first of its kind to compile and standardize massive datasets on the structure and function of mammalian brains.

Focusing on multicamera video streaming for microscopy.

This repository contains CAD (Solidworks) files for the ExA-SPIM microscope system.

This repository contains optical (ZEMAX) files for the ExA-SPIM microscope system.

This service can be used to upload data stored in a VAST drive. It uses FastAPI to upload a job submission csv file that will be used to trigger a data transfer job in an on-prem HPC. Based on the information provided in the file, the data upload process fetches the appropriate metadata and starts the upload process.

This package allows you to run compute-intense parts of BigStitcher distributed on your workstation, a cluster or the cloud using Apache Spark.

The Open Ephys GUI is an open-source, plugin-based application for acquiring extracellular electrophysiology data.

The Open Ephys GUI is designed to provide a fast and flexible interface for acquiring and visualizing data from extracellular electrodes.

The Open Ephys GUI was built by neuroscientists, for neuroscientists. It has all the features needed to acquire and visualize your data—while also making it easy to add new modules written in C++.

Code Ocean capsule to convert ephys data for IBL Ephys Alignment GUI.

Neuroglancer is a WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons).

Tool for aligning electrophysiological features to anatomical landmarks.

An open, containerized electrophysiology analysis pipeline using Kilosort via SpikeInterface. The pipeline includes preprocessing, spike sorting, postprocessing, curation based on unit quality metrics, and visualization with sortingview.

SpikeInterface is a Python framework designed to unify preexisting spike sorting technologies into a single code base.

Library for aind mri utilities.

A flexible, scalable extracellular electrophysiology rig

Parallax is a graphical user interface designed to streamline the process of setting up and performing acute in vivo electrophysiology experiments.

The Neuron Morphology Community Portal is is hub to search for whole-brain reconstructions of neuron morphologies in the adult mouse brain. It can host any data that has been aligned to the Allen Mouse Brain Common Coordinate Framework. Log into contribute new neuron skeletons or sign up to proofread new neurons with HortaCloud.