Open Tools & Data

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Portals
Portals

Neural Circuitry Underlying Detection of Local and Global Prediction Errors

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

Publications
Publications

SHIELD: Skull-shaped hemispheric implants enabling large-scale electrophysiology datasets in the mouse brain

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.

Publications
Publications

Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues

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.

Protocols
Protocols

Whole Mouse Brain Delipidation - Dichloromethane

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

Protocols
Protocols

Preparing a 3D Printed Implant for Acute In Vivo Electrophysiology V.1

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

Protocols
Protocols

General Setup and Takedown Procedures for Rodent Neurosurgery V.2

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

Protocols
Protocols

Mouse Habituation - Head Fixation on Disk

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

Protocols
Protocols

Mouse Water Restriction

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

Protocols
Protocols

Making Agarose for use in acute in vivo Electrophysiology Experiments

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

Protocols
Protocols

Plug Removal for acute 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.

Publications
Publications

Behavioral strategy shapes activation of the Vip-Sst disinhibitory circuit in visual cortex

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.

Portals
Portals

Utilizing Illusory Contours to Elucidate the Neural Mechanism of Binding

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

Publications
Publications

Deciphering neuronal variability across states reveals dynamic sensory encoding

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.

Publications
Publications

Ultra-high density electrodes improve detection, yield, and cell type identification in neuronal recordings

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.

Protocols
Protocols

Duragel Application for Acute Electrophysiology Recordings

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

Protocols
Protocols

Mounting and Coverslipping Mouse Brain Sections

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.

Protocols
Protocols

Immunohistochemistry (IHC) Staining Mouse Brain Sections

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.

Protocols
Protocols

DAPI Staining Mouse Brain Sections

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.

Protocols
Protocols

Protocol Collection: Perfusing, Sectioning, IHC, Mounting and Coverslipping Mouse Brain Specimens

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.

Protocols
Protocols

Sectioning Mouse Brain with Sliding Microtome

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

Portals
Portals

Responses to inconsistent stimuli in somata and distal apical dendrites in primary visual cortex

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

Portals
Portals

Predictive Learning and Somato-dendritic Coupling

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

Publications
Publications

OpenScope 2023 Annual Report

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.

Protocols
Protocols

SmartSPIM setup and alignment

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

Protocols
Protocols

Imaging cleared mouse brains on SmartSPIM

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.

Publications
Publications

Coordinated changes in a cortical circuit sculpt effects of novelty on neural dynamics

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.

Publications
Publications

Compression strategies for large-scale electrophysiology data

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.

Publications
Publications

Saccade-Responsive Visual Cortical Neurons Do Not Exhibit Distinct Visual Response Properties

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.

Publications
Publications

Recurrent pattern completion drives the neocortical representation of sensory inference

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.

Protocols
Protocols

Tetrahydrofuran and Dichloromethane Delipidation of a Whole Mouse Brain

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

Protocols
Protocols

Whole Mouse Brain Delipidation, Immunolabeling, and Expansion Microscopy

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.

Protocols
Protocols

Immunolabeling of a Whole Mouse Brain

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

Protocols
Protocols

Aqueous (SBiP) Delipidation of a Whole Mouse Brain

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.

Portals
Portals

Differential encoding of temporal context and expectation

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

Portals
Portals

Effects of Periodic Visual Stimulation on Neural Activity in Mouse Visual Cortex

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

Portals
Portals

Measuring Stimulus-Evoked Neurophysiological Differentiation in Distinct Populations of Neurons in 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.

Publications
Publications

Glutamate indicators with improved activation kinetics and localization for imaging synaptic transmission

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.

Publications
Publications

Stimulus novelty uncovers coding diversity in visual cortical circuits

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.

Publications
Publications

OpenScope 2022 Annual Report

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.

Publications
Publications

OpenScope 2021 Annual Report

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.

Software
Software

Open Ephys GUI

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++.

Publications
Publications

A standardized head-fixation system for performing large-scale, in vivo physiological recordings in mice

Here we report the engineering strategies that we implemented when creating the Allen Brain Observatory physiology pipelines.

Hardware
Hardware

Allen Institute Hardware

Selected design files for custom hardware for scientific instruments that we have developed for use in-house, or in partnership with collaborators.

Software
Software

Parallax

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

Hardware
Hardware

Modular Insertion System Design Files

A flexible, scalable extracellular electrophysiology rig

Software
Software

aind-mri-utils

Library for aind mri utilities.

Software
Software

SpikeInterface

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

Software
Software

Spike Sorting Pipeline

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.

Software
Software

IBL Ephys Alignment App

Tool for aligning electrophysiological features to anatomical landmarks.

Software
Software

Neuroglancer

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).

Software
Software

Data Export Capsule

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

Software
Software

BigStitcher Spark

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

Software
Software

Whole Brain Data Compression and Upload Service

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.

Software
Software

ExA-SPIM Optics

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

Hardware
Hardware

ExA-SPIM Hardware

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

Software
Software

ACQUIRE Software

Focusing on multicamera video streaming for microscopy.

Software
Software

Neuroglancer Hub

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

Portals
Portals

HortaCloud

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.

Hardware
Hardware

MBF SLAP2 Website

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.

Plasmids
Plasmids

Kaspar Podgorski Lab Materials

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.

Portals
Portals

OpenScope Data Portal

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.

Hardware
Hardware

Harp Core for the Raspberry Pi Pico

A Harp core implementation on the RP2040

Hardware
Hardware

Ephys-compatible and Harp-compliant high speed lick detector

An ephys-compliant capacitive lick detector.

Hardware
Hardware

Harp-compliant sniff sensing system

Signal conditioning board for an implanted thermistor.

Hardware
Hardware

Ephys-compatible electronic controller for a variable-friction mouse treadmill

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

Software
Software

Whole brain lightsheet microscopy processing pipeline

Repository that hosts the SmartSPIM pipeline code.

Hardware
Hardware

Schneider-Kreuznach ExA-SPIM

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.

Software
Software

2-photon cellular imaging processing pipelines

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

Software
Software

AIND Metadata Schema

A library that defines AIND data schema and validates JSON.

Portals
Portals

OpenScope Application

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

Projects

Projects aimed at understanding life and advancing health

Cell Types & Learning

We are combining longitudinal in vivo calcium imaging with spatial transcriptomics to investigate how specific cell types restructure their activity during novelty processing and task learning.

Explore project

Dynamic Routing

We are studying task-switching behaviors in mice to determine how the brain controls the flow of its own activity and how neuronal circuits are reconfigured to dynamically route information for different tasks.

Explore project

OpenScope

OpenScope provides access to cutting-edge neurophysiological methods to scientists across the world. Similar to astronomical observatories, scientists propose experiments that are then executed at the Allen Institute.

Explore project