Introduction
Demonstration to run the AutoCUTS-LM-Analysis code with pictures. The full setup with scripts and some image examples are available at .
When using the code or data you can cite: Larsen NY, Li X, Tan X, Ji G, Lin J, Rajkowska G, Møller J, Vihrs N, Sporring J, Fei S, Nyengaard JR. "Cellular 3D-reconstruction and analysis in the human cerebral cortex using automatic serial sections". Commun Biol 4, 1030, Springer Nature,10.1038/s42003-021-02548-6, (2021). https://www.nature.com/articles/s42003-021-02548-6
Requirements
Before starting, you will need the following:
- Install MATLAB.
- Install Image processing toolbox and Computer vision toolbox before running the code.
- Install R.
Code Guideline
There are five folders in this repository.
- BiopsyExtraction contains a userfriendly script to random sample biopsies from a block of tissue.
- Section_segmentation script was used to detect focused sections and export them as individual files. The script was appled on a test image.
- AutoCUTSAnalysis includes scripts implemented on a test collection of 50 images(will be available after publication of article) that involve the following steps:
- Align sections
- Crop aligned stack where only tissue appears
- Using the UNetDense architecture to segment cells, the region of interest could then be defined based on a density map of centroids.
- Filtering small cells away with k-means and reconstruct neurons in 3D.
- ValidationDeeplearning will estimate the pixelwise and objectwise validation of the UNetDense model output.
- Pictures of objectwise validation will be attach after publication.
- Look at False-Negative plot in the article for further information.
- CylindricalKfunction Demonstration to run the cylindrical K-function code with pictures. The function was introduced in 'The cylindrical K-function and Poisson line cluster point processe' by Jesper Møller et al. All credits go to the script writer, Ninna Vihrs.
- The code analyses the columnar structure in 3D point patterns for one test subject.
- Pictures will be attach after publication.
Contact
If you have any questions or suggestions, you can reach Nick via e-mail at nick.yin.larsen@gmail.com for the MATLAB scripts or Ninna via e-mail at nvihrs@math.aau.dk for the R-script.
Citation
If using this dataset, please cite:
@Article{NYLCOM,
author = {NY Larsen and X Li and X Tan and G Ji and J Lin and G Rajkowska and J Møller and N Vihrs and J Sporring and F Sun and JR Nyengaard},
journal = {Communication Biology (in press)},
title = {Cellular 3D-reconstruction and analysis in the human cerebral cortex using automatic serial sections},
year = {2021},
number = {4},
volume = {1030},
doi = {10.1038/s42003-021-02548-6},
publisher = {Springer Nature},
}