Nov 04, 2025
Brain CABLE analysis
- Yue Zhang1,
- Tao Song2,
- Chao-Yu Yang1,
- Pengcheng Zhou1,
- Guo-Qiang Bi1,
- Yanyang Xiao1,
- Cirong Liu2,
- Fang Xu1
- 1Shenzhen Institutes of Advanced Technology, Chinese Academy of Science;
- 2Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences
Protocol Citation: Yue Zhang, Tao Song, Chao-Yu Yang, Pengcheng Zhou, Guo-Qiang Bi, Yanyang Xiao, Cirong Liu, Fang Xu 2025. Brain CABLE analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.5qpvoo5zdv4o/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: April 03, 2025
Last Modified: November 04, 2025
Protocol Integer ID: 126064
Keywords: Tractography, Fiber tract, Primate brain, structural connectivity mapping of primate brain, brain cable analysis, brain cable analysis this protocol, fiber tracts in the brain, enhancing structural connectivity mapping, fiber tract, cytoarchitecture, primate brain, 3d microscopy, cellular resolution, imaging data, cable, data of mouse, human brain, spatial arrangement of adjacent cell, fiber, bending fiber, link estimation, resolution imaging dataset, adjacent cell, resolution fluorescence
Funders Acknowledgements:
Youth Innovation Promotion Association CAS grant
Grant ID: 2022367
Shenzhen Medical Research Funds grant
Grant ID: A2303005
Shenzhen Science and Technology Program
Grant ID: RCYX20210706092100003
STI 2030-Major Projects
Grant ID: 2022ZD0205203
Abstract
This protocol is for using the cytoarchitecture-based link estimation (CABLE) method to infer fiber tracts in the brain by analyzing nuclear/somal anisotropy and spatial arrangement of adjacent cells. This method was developed based on the high-resolution fluorescence imaging data of mouse, marmoset, macaque, and human brains obtained with the serial sectioning-and-clearing, 3D microscopy, semi-automated reconstruction and tracing (SMART) strategy. CABLE effectively resolves intersecting and bending fibers, enhancing structural connectivity mapping of primate brains to the cellular resolution. The method is compatible with other micrometer-resolution imaging datasets, provided the cytoarchitecture is labeled via nuclear or somal staining.
Troubleshooting
CABLE analysis for 3D images
Obtain 3D-reconstructed brain images
We recommend the SMART brain mapping pipeline for obtaining the 3D whole-brain images, with a spatial resolution of 1 μm × 1μm × 2.5μm.
(optional) Get the ground-truth virus-labeling axons.
3D imaging with other methods is also applicable, given the spatial resolution is beyond 5 μm.
Convert the image to a single HDF5 file.
Run the CABLE analysis tool available at: BrainCABLE/CABLE
CABLE analysis for 2D images
5m
5m
Open a 2D brain image in Fiji. Navigate to Plugins–OrientationJ–Orientation vector field.
DAPI staining of the corpus callosum.
Orientation vector field analysis window.
(optional) Apply a Gaussian blur with a kernel size of 1 or 2μm for denoising.
Configure the structure tensor analysis window and vector field window size based on the scale under analysis.
Enable the “overlay” and “show table” options. This will display the local orientation on the image and present quantitation results in a pop-up table.
The red lines represent the local directions.
Corresponding to the relevant attributes of each line segment.
Protocol references
1. Xu, F. et al. High-throughput mapping of a whole rhesus monkey brain at micrometer
resolution. Nat. Biotechnol. 39, 1521–1528 (2021).
2. Schurr, R. & Mezer, A. A. The glial framework reveals white-matter fiber architecture in human and
primate brains. Science 374, 762–767 (2021).