Article Figures & Data
Figures
- Figure 1
Workflow of reconstructing or editing a neuron structure in the SWC framework, which defines GUI software that takes either a raw image or an SWC file as input and generates an acceptable neuron structure through user interactions. The user can save the neuron structure into standard SWC files during or after reconstruction.
- Figure 2
neuTube 1.0 is a GUI application built upon four major modules: 2D visualization, 3D visualization, image analysis, and neuron structure operation.
- Figure 3
Tracing and editing interface of neuTube 1.0. A, Interactive tracing in 2D view. B, 2D view of SWC nodes. On-plane and off-plane nodes are distinguished by color saturation and transparency. A node with a yellow bounding box indicates that it is selected. C, The context menu for editing in the 2D view, which can be triggered by a right mouse click. D, Interactive tracing in 3D view. E, 3D visualization of the tracing results. Branch nodes and terminal nodes are shown in green and yellow colors, respectively. Selected nodes are shown with their bounding boxes. F, The context menu for editing in the 3D view. G, A neuron shown as connected tubes. H, A neuron shown as lines.
- Figure 4
Examples of high-level operations of neuTube 1.0. To illustrate the operation, we visualize the nodes of a neuron in different colors according to the topology: blue for root nodes, green for branch nodes, yellow for leaf nodes, and red for other nodes. Selected nodes are highlighted by a yellow bounding box. For the corresponding operation as named in each row, the panels on the left (A, C, E, G, I, K) show the selected nodes to operate and the panels on the right (B, D, F, H, J, L) show the result of operation.
- Figure 5
neuTube 1.0 helps produce significantly more accurate neuron structures than Neuromantic and Neurostudio do. A, Nodeg is a critical point from ground truth neuron and Nodet is a critical point from tracing result. These two points can be matched when
because the distance between them is less than
. They cannot be matched when
. B, The solid curves show average errors measuring the discrepancy between the critical point sets from user reconstruction and ground truth under different distance thresholds. The surrounding envelopes are the 95% confidence intervals. The error curve of neuTube 1.0 (green) is consistently lower than the other two, with p < 0.01 (t test) when
(compared to Neurostudio) or
(compared to Neuromantic). - Figure 6
Mapping brain connectivity with neuTube 1.0. A, The original 3D confocal image contains postsynaptic neurons. B, The target neuron (green) was traced semi-automatically. The red branches belong to background neurons. C, mGRASP-labeled synapses (yellow) were detected automatically, with sizes enlarged for better visualization. D, The synapses were mapped to the target neuron (green) and background neurons (red).
Tables
Software Undo/Redo 2D editing 3D editing 3D image interaction 2D neuron visualization 3D visualization neuTube 1.0 Unlimited Yes Yes Yes Slice-by-slice Volume and neuron structure Neuromantic 1 step Yes Limitedb No Slice-by-slice Neuron structure Neurostudio 1 step Limiteda Limitedb No Projection Volume and neuron structure a Cannot change node size.
b No topological operation.
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