Functional connectomics spanning multiple areas of mouse visual cortex

Abstract

The value of an integrated approach for understanding the neocortex by combining functional characterization of single neuron activity with the underlying circuit architecture has been understood since the dawn of modern neuroscience. However, in practice, anatomical connectivity and physiology have been studied mostly separately. Following in the footsteps of previous studies that have combined physiology and anatomy in the same tissue, here we present a unique functional connectomics dataset that contains calcium imaging of an estimated 75,000 neurons from primary visual cortex (VISp) and three higher visual areas (VISrl, VISal and VISlm), that were recorded while a mouse viewed natural movies and parametric stimuli. The functional data were co-registered with electron microscopy (EM) data of the same volume which were automatically segmented, reconstructing more than 200,000 cells (neuronal and non-neuronal) and 524 million synapses. Subsequent proofreading of some neurons in this volume yielded reconstructions that include complete dendritic trees as well the local and inter-areal axonal projections. The largest proofread excitatory axon reached a length of 19 mm and formed 1,893 synapses, while the largest inhibitory axon formed 10,081 synapses. Here we release this dataset as an open access resource to the scientific community including a set of analysis tools that allows easy data access, both programmatically and through a web user interface.

3D reconstruction of cell nuclei in a full Drosophila brain

“…Somas of a specific cell or cell group can be used as anatomical landmarks (Wyman et al, 1984). The morphology of cell nuclei may be helpful for cell type classification (MICrONS Consortium et al, 2021).…”

A Scalable and Modular Automated Pipeline for Stitching of Large Electron Microscopy Datasets

“…After resin embedding, ultrathin sections (40 nm or 45 nm) were manually cut in a Leica UC7 ultra-microtome and a RMC Atumtome. After sectioning, the samples were loaded into the automated Transmission Electron Microscopes (autoTEM) and we followed the TEM operation routine (described in [1] and [25]) to bring up the HT voltage and filament current and then align the beam. Calibration of the autoTEM involved tape and tension calibration for bar-code reading, measuring beam rotation and camera pixels, and stage alignment.…”

“…Figure 2 shows the specialized services that facilitate data transfer and tracking from high-throughput microscopes to shared compute resources. This infrastructure was used to process multiple petascale datasets, including a 1 mm 3 (mouse dataset 1) of the mouse brain that is publicly available on microns-explorer.com [25]. Over 26,500 sections were imaged at 4 nm/pixel resolution using 5 microscopes, running in a continuous and automated fashion [1].…”

“…We also implemented a workflow engine that executes the volume assembly workflow in an automated fashion triggered following the transfer of raw data. ASAP has been successfully utilized for continuous processing of several large-scale datasets of the mouse visual cortex and human brain samples including one cubic millimeter of mouse visual cortex [1,25]. The pipeline also has multi-channel processing capabilities and can be applied to fluorescence and multi-modal datasets like array tomography.…”

“…The entire software pipeline includes a complete set of tools for stitching, automated quality control, 3D section alignment, and final rendering of the assembled volume to disk. ASAP has been deployed for continuous processing of several large-scale datasets of the mouse visual cortex and human brain samples including one cubic millimeter of mouse visual cortex [1,25] at speeds that exceed imaging. The pipeline also has multi-channel processing capabilities and can be applied to fluorescence and multi-modal datasets like array tomography.…”