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[[License: BSD 3-Clause](https://img.shields.io/badge/License-BSD* is a free and open-source R package for (high-throughput) axonal integrity analysis of micrographs, such as murine dorsal root ganglia explant cultures. AiES offers tools to segment neurites, extract quantitative features, generate SVM models, and quantify axon integrity. It is released under the BSD 3-Clause License.
Before installing the AiES package or EBImage on Linux, please run:
sudo apt-get update
sudo apt-get install -y libtiff5-dev libjpeg-dev libpng-dev
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
::install("EBImage")
BiocManager
# Install from CRAN (when available)
# install.packages("AiES")
# Or install the development version from GitHub
# install.packages("devtools")
#devtools::install_github("BreezyCave/AiES")
AiES provides an integrated workflow for axon image analysis, including feature extraction, machine learning classification, and quantitative assessment. The main functions are:
axDistmap()
: Extracts morphological features from axon
images (TIFF image files).axSvm()
: Builds an SVM classifier utilizing extracted
features.axQnt()
: Quantifies Axon Integrity Index (AII) and
Degeneration Index (DI) for new data using a trained SVM.For detailed usage instructions, please refer to the vignettes included in the package.
library(AiES)
# Specify sample image folders included in the package
<- system.file("extdata", "Degenerate_Images", package = "AiES")
img_dir1 <- system.file("extdata", "Intact_Images", package = "AiES")
img_dir2
# Extract features from multiple folders (recursive search)
axDistmap(
folder_paths = c(img_dir1, img_dir2),
subBack = 30,
resizeW = 900,
output_path = tempdir()
)
axDistmap(
folder_paths = img_dir1,
allFeatures = TRUE,
output_path = tempdir()
)
This function processes all TIFF files in the selected directories, generating for each image: - A distance map image - A binary image (optional) - A text file containing feature data
<- system.file("extdata", "Degenerate_txt", package = "AiES")
Degenerate_dir <- system.file("extdata", "Intact_txt", package = "AiES")
Intact_dir
axSvm(
degenerate_path = Degenerate_dir,
intact_path = Intact_dir,
output_data_path = tempdir(),
output_model_path = tempdir(),
nCst = 3, nGmm = 0.1, nCrss = 5
)
This function generates: - An extracted data file for machine learning - A trained SVM model file
<- system.file("extdata", "Degenerate_Images", package = "AiES")
img_dir1 <- system.file("extdata", "Intact_Images", package = "AiES")
img_dir2
<- axQnt(
result input_dir = c(img_dir1, img_dir2),
svm_model_path = system.file("extdata", "svm_example_model.svm", package = "AiES"),
output_dir = tempdir()
)
# Visualize the results
library(ggplot2)
ggplot(result, aes(x = AxonIntegrityIndex)) +
geom_histogram(binwidth = 0.1, fill = "blue", alpha = 0.7) +
ggtitle("AII Distribution")
This function generates: - A summary CSV file containing the Axon Integrity Index and Degeneration Index for each image - (Optional) Single image prediction data files
AiES is licensed under the BSD 3-Clause License. See the LICENSE file for details.
This package makes use of the following R packages, each with its own license:
Users must comply with the license terms of these dependencies when
redistributing or modifying this package.
See each package’s CRAN/Bioconductor page for full license texts.
If you use AiES in your research, please cite:
Tokunaga S, Funakoshim M, Araki T (2025). AiES: Axon Integrity Evaluation System. R package version 0.99.5. https://github.com/BreezyCave/AiES
For bug reports or feature requests, please use the Issues page on GitHub.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.