Webknossos (stylized in all caps) is an open-source software [1] and online platform for viewing, annotating, and sharing large 3D images, primarily used by neuroscientists and cell biologists. It is capable of handling massive volume microscopy datasets, making it a valuable tool in the field of connectomics.
Webknossos was developed by the company scalable minds in close collaboration with the Max Planck Institute for Brain Research, specifically with the Department of Connectomics led by Moritz Helmstaedter. [2] It was designed to address the challenges of data analysis in connectomics. With the advancement of volume electron microscopy (vEM), datasets have expanded to sizes ranging from tens of terabytes (TB) to petabytes (PB), rendering the distribution of data on physical hard drives to numerous annotators impractical. The platform was conceived to facilitate efficient and distributed 3D data annotation for PB-sized datasets directly in web browsers.
The software has been used in a number of applications for neuroscience research.
Webknossos facilitates both sparse and dense neuron reconstruction. [3] Sparse annotations, generated with the skeleton annotation tools, can serve as evaluation data for assessing the performance of automated reconstruction models. For dense neuron reconstruction, researchers manually annotate neurons using volume annotation tools. This annotated data then frequently serves as ground truth for training Machine Learning models. [4] The proofreading tools in Webknossos then assist in correcting split and merge errors through a supervoxel graph.
Webknossos has been employed in several microscale connectomic research projects. [5] [6] Typically, after completing neuron reconstruction, users perform automated synapse detection following a similar workflow. They manually annotate synapses in Webknossos, train models on this data, and then apply these models to their datasets. The results are compared against the ground truth and can be refined. This process is also applied to neuron type identification. Once synapses and neuron types are detected, users can generate a connectome and explore it interactively in Webknossos. The platform allows users to click on a neuron to list all synaptic partners and view each synapse in the electron microscopy (EM) data.
Webknossos is utilized to correct errors in automated reconstructions from deep learning systems. [7] The provided proof-reading tools allow users to explore reconstructed cells in 3D, identify merge or split errors, closely examine the mistakes in the EM data, and correct segments by splitting or merging them.
The skeleton tools in Webknossos enable users to trace the morphology of neurons by creating trees with nodes and branch points, facilitating detailed neuronal tracing. With its unique Flight Mode feature, users can trace axons or dendrites at significantly higher speeds then conventional methods. [2]
Webknossos has been used for the annotation and reconstruction of cells from various species, including mice, humans, macaques, drosophila, and more. Notable scientific studies that published their datasets as open access on Webknossos include:
Neuropil is any area in the nervous system composed of mostly unmyelinated axons, dendrites and glial cell processes that forms a synaptically dense region containing a relatively low number of cell bodies. The most prevalent anatomical region of neuropil is the brain which, although not completely composed of neuropil, does have the largest and highest synaptically concentrated areas of neuropil in the body. For example, the neocortex and olfactory bulb both contain neuropil.
A dendritic spine is a small membrane protrusion from a neuron's dendrite that typically receives input from a single axon at the synapse. Dendritic spines serve as a storage site for synaptic strength and help transmit electrical signals to the neuron's cell body. Most spines have a bulbous head, and a thin neck that connects the head of the spine to the shaft of the dendrite. The dendrites of a single neuron can contain hundreds to thousands of spines. In addition to spines providing an anatomical substrate for memory storage and synaptic transmission, they may also serve to increase the number of possible contacts between neurons. It has also been suggested that changes in the activity of neurons have a positive effect on spine morphology.
The olfactory bulb is a neural structure of the vertebrate forebrain involved in olfaction, the sense of smell. It sends olfactory information to be further processed in the amygdala, the orbitofrontal cortex (OFC) and the hippocampus where it plays a role in emotion, memory and learning.
Pyramidal cells, or pyramidal neurons, are a type of multipolar neuron found in areas of the brain including the cerebral cortex, the hippocampus, and the amygdala. Pyramidal cells are the primary excitation units of the mammalian prefrontal cortex and the corticospinal tract. One of the main structural features of the pyramidal neuron is the conic shaped soma, or cell body, after which the neuron is named. Other key structural features of the pyramidal cell are a single axon, a large apical dendrite, multiple basal dendrites, and the presence of dendritic spines.
Mitral cells are neurons that are part of the olfactory system. They are located in the olfactory bulb in the mammalian central nervous system. They receive information from the axons of olfactory receptor neurons, forming synapses in neuropils called glomeruli. Axons of the mitral cells transfer information to a number of areas in the brain, including the piriform cortex, entorhinal cortex, and amygdala. Mitral cells receive excitatory input from olfactory sensory neurons and external tufted cells on their primary dendrites, whereas inhibitory input arises either from granule cells onto their lateral dendrites and soma or from periglomerular cells onto their dendritic tuft. Mitral cells together with tufted cells form an obligatory relay for all olfactory information entering from the olfactory nerve. Mitral cell output is not a passive reflection of their input from the olfactory nerve. In mice, each mitral cell sends a single primary dendrite into a glomerulus receiving input from a population of olfactory sensory neurons expressing identical olfactory receptor proteins, yet the odor responsiveness of the 20-40 mitral cells connected to a single glomerulus is not identical to the tuning curve of the input cells, and also differs between sister mitral cells. Odorant response properties of individual neurons in an olfactory glomerular module. The exact type of processing that mitral cells perform with their inputs is still a matter of controversy. One prominent hypothesis is that mitral cells encode the strength of an olfactory input into their firing phases relative to the sniff cycle. A second hypothesis is that the olfactory bulb network acts as a dynamical system that decorrelates to differentiate between representations of highly similar odorants over time. Support for the second hypothesis comes primarily from research in zebrafish.
Brain mapping is a set of neuroscience techniques predicated on the mapping of (biological) quantities or properties onto spatial representations of the brain resulting in maps.
Winfried Denk is a German physicist. He built the first two-photon microscope while he was a graduate student in Watt W. Webb's lab at Cornell University, in 1989.
A connectome is a comprehensive map of neural connections in the brain, and may be thought of as its "wiring diagram". An organism's nervous system is made up of neurons which communicate through synapses. A connectome is constructed by tracing the neuron in a nervous system and mapping where neurons are connected through synapses.
Connectomics is the production and study of connectomes: comprehensive maps of connections within an organism's nervous system. More generally, it can be thought of as the study of neuronal wiring diagrams with a focus on how structural connectivity, individual synapses, cellular morphology, and cellular ultrastructure contribute to the make up of a network. The nervous system is a network made of up to billions of connections and these connections are responsible for our thoughts, emotions, actions, memories, function and dysfunction. Therefore, the study of connectomics aims to advance our understanding of mental health and cognition by understanding how cells in the nervous system are connected and communicate. Because these structures are extremely complex, methods within this field use a high-throughput application of functional and structural neural imaging, most commonly magnetic resonance imaging (MRI), electron microscopy, and histological techniques in order to increase the speed, efficiency, and resolution of these nervous system maps. To date, tens of large scale datasets have been collected spanning the nervous system including the various areas of cortex, cerebellum, the retina, the peripheral nervous system and neuromuscular junctions.
Serial block-face scanning electron microscopy is a method to generate high resolution three-dimensional images from small samples. The technique was developed for brain tissue, but it is widely applicable for any biological samples. A serial block-face scanning electron microscope consists of an ultramicrotome mounted inside the vacuum chamber of a scanning electron microscope. Samples are prepared by methods similar to that in transmission electron microscopy (TEM), typically by fixing the sample with aldehyde, staining with heavy metals such as osmium and uranium then embedding in an epoxy resin. The surface of the block of resin-embedded sample is imaged by detection of back-scattered electrons. Following imaging the ultramicrotome is used to cut a thin section from the face of the block. After the section is cut, the sample block is raised back to the focal plane and imaged again. This sequence of sample imaging, section cutting and block raising can acquire many thousands of images in perfect alignment in an automated fashion. Practical serial block-face scanning electron microscopy was invented in 2004 by Winfried Denk at the Max-Planck-Institute in Heidelberg and is commercially available from Gatan Inc., Thermo Fisher Scientific (VolumeScope) and ConnectomX.
The name granule cell has been used for a number of different types of neurons whose only common feature is that they all have very small cell bodies. Granule cells are found within the granular layer of the cerebellum, the dentate gyrus of the hippocampus, the superficial layer of the dorsal cochlear nucleus, the olfactory bulb, and the cerebral cortex.
IMOD is an open-source, cross-platform suite of modeling, display and image processing programs used for 3D reconstruction and modeling of microscopy images with a special emphasis on electron microscopy data. IMOD has been used across a range of scales from macromolecule structures to organelles to whole cells and can also be used for optical sections. IMOD includes tools for image reconstruction, image segmentation, 3D mesh modeling and analysis of 2D and 3D data.
ilastik is a user-friendly free open source software for image classification and segmentation. No previous experience in image processing is required to run the software. Since 2018 ilastik is further developed and maintained by Anna Kreshuk's group at European Molecular Biology Laboratory.
Neuronal tracing, or neuron reconstruction is a technique used in neuroscience to determine the pathway of the neurites or neuronal processes, the axons and dendrites, of a neuron. From a sample preparation point of view, it may refer to some of the following as well as other genetic neuron labeling techniques,
A Drosophila connectome is a list of neurons in the Drosophila melanogaster nervous system, and the chemical synapses between them. The fly's nervous system consists of the brain plus the ventral nerve cord, and both are known to differ considerably between male and female. Dense connectomes have been completed for the female adult brain, the male nerve cord, and the female larval stage. The available connectomes show only chemical synapses - other forms of inter-neuron communication such as gap junctions or neuromodulators are not represented. Drosophila is the most complex creature with a connectome, which had only been previously obtained for three other simpler organisms, first C. elegans. The connectomes have been obtained by the methods of neural circuit reconstruction, which over the course of many years worked up through various subsets of the fly brain to the almost full connectomes that exist today.
Vaa3D is an Open Source visualization and analysis software suite created mainly by Hanchuan Peng and his team at Janelia Research Campus, HHMI and Allen Institute for Brain Science. The software performs 3D, 4D and 5D rendering and analysis of very large image data sets, especially those generated using various modern microscopy methods, and associated 3D surface objects. This software has been used in several large neuroscience initiatives and a number of applications in other domains. In a recent Nature Methods review article, it has been viewed as one of the leading open-source software suites in the related research fields. In addition, research using this software was awarded the 2012 Cozzarelli Prize from the National Academy of Sciences.
Neural circuit reconstruction is the reconstruction of the detailed circuitry of the nervous system of an animal. It is sometimes called EM reconstruction since the main method used is the electron microscope (EM). This field is a close relative of reverse engineering of human-made devices, and is part of the field of connectomics, which in turn is a sub-field of neuroanatomy.
The MICrONS program is a five-year project run by the United States government through the Intelligence Advanced Research Projects Activity (IARPA) with the goal of reverse engineering one cubic millimeter—spanning many petabytes of volumetric data—of a rodent's brain tissue and use insights from its study to improve machine learning and artificial intelligence by constructing a connectome. The program is part of the White House BRAIN Initiative.
An axo-axonic synapse is a type of synapse, formed by one neuron projecting its axon terminals onto another neuron's axon.
Patch-sequencing (patch-seq) is a modification of patch-clamp technique that combines electrophysiological, transcriptomic and morphological characterization of individual neurons. In this approach, the neuron's cytoplasm is collected and processed for RNAseq after electrophysiological recordings are performed on it. The cell is simultaneously filled with a dye that allows for subsequent morphological reconstruction.