sepehrband / AxonDiameter

ActiveAx with ultra-high gradient strength

Axon diameter mapping of mouse corpus callosum

This link is provided in accordance with the following articles:

Towards Higher Sensitivity And Stability Of Axon Diameter Estimation With Diffusion-Weighted Magnetic Resonance Imaging
Farshid Sepehrband, Daniel C. Alexander, Nyoman D. Kurniawan, David C. Reutens, and Zhengyi Yang
NMR in Biomedicine 29(3):293-308. DOI: 10.1002/nbm.3462, link

Parametric Probability Distribution Functions for Axon Diameters of Corpus Callosum
Farshid Sepehrband, Daniel C. Alexander, Kristi A. Clark, Nyoman D. Kurniawan, Zhengyi Yang and David C. Reutens Frontiers in Neuroanatomy, 10:59. DOI: 10.3389/fnana.2016.00059 link

Supplementary material 🔬🐁

Diffusion-weighted MRI data (ActiveAx with G_max = 1.35 T/m)

Two datasets were acquired in this study, which are made available here:

• 3-shell data can be downloaded here.
• 5-shell data can be downloaded here.
• gradient encoding directions can be found here.

For information regarding the acquisition protocol please see the above article.

Electron Microscopy (EM) data

• Raw electron microscopy images can be found here.
• Manually segmented axons (in MATLAB format) can be found here.
• Axon diameter values in micrometer (in CSV format) can be found here.

** Note that some of the images were excluded from axon diameter estimation, due to low image quality. However they are included in the link above (raw EM images), as they may be useful for other purposes.

MATLAB demo (EM analysis)

%% input raw material and show them
I = imread('Path-to-EM-data/Raw/Genu/ccleftb1_5k.tif');
laod('Path-to-EM-data/MATfiles/ccleftb1_5k.mat');
figure(1);subplot(1,2,1);imshow(I,[]);
subplot(1,2,2);imshow(ccleftb1_5k.AllCircles);

%% extract axon diameter distribution and plot it
bwComp = bwconncomp(ccleftb1_5k.AllCircles);
pixelSize = (0.023);
for i = 1:length(bwComp.PixelIdxList)
    temp = bwComp.PixelIdxList(i);
    Volume(i) = length(temp{1}).*(pixelSize^2);
    Dia(i) = 2*sqrt(Volume(i)/pi);
end
figure(2);histogram(Dia)
grid on
title('Axon Diameter Distribution (ADD) of demo image')
set(gca,'LineWidth',1,'FontSize',12,'FontWeight','Bold','FontName','Arial'); 
xlabel('Axon diameter \fontsize{9}(\mum)','FontSize',12,'FontName','Arial'); 
ylabel('Frequency','FontSize',12,'FontName','Arial');