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Abstract As the serial section community transitions to volume electron microscopy, tools are needed to balance rapid segmentation efforts with documenting the fine detail of structures that support cell function. New annotation applications should be accessible to users and meet the needs of the neuroscience and connectomics communities while also being useful across other disciplines. Issues not currently addressed by a single, modern annotation application include: 1) built-in curation systems with utilities for expert intervention to provide quality assurance, 2) integrated alignment features that allow for image registration on-the-fly as image flaws are discovered during annotation, 3) simplicity for non-specialists within and beyond the neuroscience community, 5) a system to store experimental meta-data with annotation data in a way that researchers remain masked regarding condition to avoid potential biases, 6) local management of large datasets, 7) fully open-source codebase allowing development of new tools, and more. Here, we present PyReconstruct, a modern successor to the Reconstruct annotation tool. PyReconstruct operates in a field-agnostic manner, runs on all major operating systems, breaks through legacy RAM limitations, features an intuitive and collaborative curation system, and employs a flexible and dynamic approach to image registration. It can be used to analyze, display, and publish experimental or connectomics data. PyReconstruct is suited for generating ground truth to implement in automated segmentation, outcomes of which can be returned to PyReconstruct for proofreading and quality control. Significance statementIn neuroscience, the emerging field of connectomics has produced annotation tools for reconstruction that prioritize circuit connectivity across microns to centimeters and farther. Determining the strength of synapses forming the connections is crucial to understand function and requires quantification of their nanoscale dimensions and subcellular composition. PyReconstruct, successor to the early annotation tool Reconstruct, meets these requirements for synapses and other structures well beyond neuroscience. PyReconstruct lifts many restrictions of legacy Reconstruct and offers a user-friendly interface, integrated curation, dynamic alignment, nanoscale quantification, 3D visualization, and more. Extensive compatibility with third-party software provides access to the expanding tools from the connectomics and imaging communities.
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A Survey of Visualization and Analysis in High‐Resolution Connectomics
Abstract The field of connectomics aims to reconstruct the wiring diagram of Neurons and synapses to enable new insights into the workings of the brain. Reconstructing and analyzing the Neuronal connectivity, however, relies on many individual steps, starting from high‐resolution data acquisition to automated segmentation, proofreading, interactive data exploration, and circuit analysis. All of these steps have to handle large and complex datasets and rely on or benefit from integrated visualization methods. In this state‐of‐the‐art report, we describe visualization methods that can be applied throughout the connectomics pipeline, from data acquisition to circuit analysis. We first define the different steps of the pipeline and focus on how visualization is currently integrated into these steps. We also survey open science initiatives in connectomics, including usable open‐source tools and publicly available datasets. Finally, we discuss open challenges and possible future directions of this exciting research field.
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- PAR ID:
- 10406071
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Computer Graphics Forum
- Volume:
- 41
- Issue:
- 3
- ISSN:
- 0167-7055
- Format(s):
- Medium: X Size: p. 573-607
- Size(s):
- p. 573-607
- Sponsoring Org:
- National Science Foundation
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