dendritic-spine-shape-analysis

Dendritic spine analysis tool for dendritic spine image segmentation, dendritic spine morphologies extraction,analysis and clustering.

System requirements

• Windows 8 or newer
• Minimum 1GB RAM
• Minimum 6 GB disk space

Install

1. Download code
2. Unzip CGAL files next to code, e.g. PATH_TO_CODE\CGAL\...
3. Install Anaconda
4. Open Anaconda
5. Execute

cd PATH_TO_CODE
conda create --name spine-analysis -c conda-forge --file requirements.txt -y

Run

1. Open Anaconda
2. Execute

cd PATH_TO_CODE
conda activate spine-analysis
jupyter notebook

Example datasets

example_dendrite

Dataset consist of a .tif image of a dendrite, 22 polygonal meshes of dendrite spines and a dendrite polygonal mesh computed with dendrite-segmentation.ipynb notebook. This example dataset provides a demonstration of dendrite image segmentation performance and functionality of the methods from the Utilities.ipynb notebook.

0.025 0.025 0.1 dataset

Dataset consists of 270 polygonal meshes of dendrite spines related to 54 dendrites and of 54 polygonal meshes for dendrites computed with dendrite-segmentation.ipynb notebook. A dataset subdirectory named "manual_classification" contains the expert markups from 8 people obtained using the spine-manual-classification.ipynb and the results of merging the classifications to obtain a consensus classification. This example dataset provides a demonstration of dendrite spines classification and clustering performance and functionality of the methods from the Utilities.ipynb notebook.