Journal
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
Volume 28, Issue 12, Pages 4951-4965Publisher
IEEE COMPUTER SOC
DOI: 10.1109/TVCG.2021.3109460
Keywords
Neurites; Image segmentation; Three-dimensional displays; Rendering (computer graphics); Microscopy; Image reconstruction; Visualization; Wide-field microscopy; neuron morphology; segmentation; registration; hybrid volume rendering; CNN
Categories
Funding
- NSF [CNS1650499, OAC1919752, ICER1940302, IIS2107224]
- Intramural Research Program of NIH, NINDS
- NIH, NIMH
Ask authors/readers for more resources
NeuroConstruct is a novel end-to-end application for the segmentation, registration, and visualization of brain volumes imaged using wide-field microscopy. It offers various annotation helper functions for precise and effective neurite annotation, as well as automatic neurite segmentation using convolutional neural networks. The application also includes tools for visualizing neurites and aligning serially sectioned samples.
We introduce NeuroConstruct, a novel end-to-end application for the segmentation, registration, and visualization of brain volumes imaged using wide-field microscopy. NeuroConstruct offers a Segmentation Toolbox with various annotation helper functions that aid experts to effectively and precisely annotate micrometer resolution neurites. It also offers an automatic neurites segmentation using convolutional neuronal networks (CNN) trained by the Toolbox annotations and somas segmentation using thresholding. To visualize neurites in a given volume, NeuroConstruct offers a hybrid rendering by combining iso-surface rendering of high-confidence classified neurites, along with real-time rendering of raw volume using a 2D transfer function for voxel classification score versus voxel intensity value. For a complete reconstruction of the 3D neurites, we introduce a Registration Toolbox that provides automatic coarse-to-fine alignment of serially sectioned samples. The quantitative and qualitative analysis show that NeuroConstruct outperforms the state-of-the-art in all design aspects. NeuroConstruct was developed as a collaboration between computer scientists and neuroscientists, with an application to the study of cholinergic neurons, which are severely affected in Alzheimer's disease.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available