Software to calculate vessel distributions in tissues

The following ImageJ macros allow to calculate the distribution state of a set of elements on the basis of their space-filling properties.
For theoretical background see M. Righi et al. Laboratory Investigation, 2009; 89(9); doi:10.1038/labinvest.2009.76.
For additional information, comments, problems or improvements please contact the author:
M.Righi - Institute of Neuroscience, CNR - via Vanvitelli 32, 20129 Milano - Italy. E-mail: m.righi@in.cnr.it.

Disclaimer: The software in these pages is experimental. Use these macro at your own risk. Although I am confident that they run as intended, there may be bugs and unexpected behaviour in instances that I have not envisaged. Copyright notice: You can consider the macros in this page as free software: you can redistribute it and/or modify it under the terms of the GNU General Public license as published by the Free Software Foundation; either version 2 of the license, or (at your option) any later version. These programs are distributed in the hope that they will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. To receive a copy of the GNU General Public License write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

These macros require ImageJ v. 1.38a or higher. Follow the link to update to the latest version of the ImageJ ij.jar file

Single Folder

Analyzing a set of images in a folder

• This macro calculates the distribution/space-filling indexes (H) of black pixels for each bitmap image of a set, grouped in a folder. H indexes are calculated through alternated convolutions of 3x3 square and cross kernels. Two permeation curves are constructed starting with one or the other kernel and results are interpolated to obtain index values. The macro is limited to the analysis of images with H indexes lower than 500.


• The percentage of initial black pixels is calculated for every image (binary - inverted LUT) of the folder and the maximal value obtained is set as the normalization value.


• The macro generates an output .txt file reporting the normalization value, initial area covered by black pixels together with raw and normalized H90%, H95% and H99% indexes.


• Version 1.1 created 07.03.2008

<Download macro> <Instructions> How to operate the macro, and its logic
<Macro test> an archived file to be unzipped in a folder containing 5 images.
<Results of Macro test> a .txt file with the results for the downloaded images.

Multi Folders

Analyzing multiple folders grouped in a folder

• The advantage of this macro resides in the possibility to analyze a number of indipendent folders, each containing a set of images, nested in a higher level folder. Image normalization is calculated indipendently for each folder. To normalize the H-index of all images in all folders against a common (maximal) value it is suggested to add the image showing that value to each single folder to be analyzed.


• This macro generates a number of output .txt files, one for each analyzed folder, reporting the same type of data as in the single-folder macro.


• Version 1.0 created 31.07.2008

<Download macro> <Instructions> Not yet available, sorry!.
<Macro test> an archived file to be unzipped in a folder containing 10 images in 3 different folders.
<Results of Macro test> an archived file with a result folder containing 3 results file, one for each of the analyzed folders.

Toolbox Section

Utility macros

• < GetInitialAreas > This macro calculates the largest percent value of foreground (black) pixels in a set of images grouped in a folder


• This macro generates an output .txt file reporting the normalization value and the initial area covered by black pixels for a group of images in a folder.


• Version 1.0 created 29.07.2008

<Download macro> <Instructions> Not yet available, sorry!.