#IMAGEJ SOFTWARE REFERENCE INSTALL#
#IMAGEJ SOFTWARE REFERENCE ARCHIVE#
#IMAGEJ SOFTWARE REFERENCE CODE#

BoneJ was dependent on third-party software that was no longer maintained, while users found they could not install and run BoneJ in their environment creating a risk of forced obsolescence.Īt the same time, the developments in ImageJ2 and Fiji represented an opportunity to improve BoneJ’s engineering standard and user experience, as well as opening avenues for new algorithm development and implementation.

At the same time the JRE version 6 that BoneJ was built for was phased out, the 3D libraries BoneJ’s plugins relied on (Java3D 1.5) were obsoleted, and the 3D Viewer 9 that BoneJ used for surface meshing and visualisation was abandoned. Schindelin and others implemented a software updater for ImageJ as part of their Fiji Is Just ImageJ ( Fiji) project 7, while ImageJ2 introduced a new N-dimensional image model and modern development practices such as modularity, dependency management ( Maven), continuous integration (Jenkins, then Travis, likely to be superseded by GitHub Actions), and community development and support protocols (GitHub, Gitter, image.sc forum) 8. In the time since BoneJ was released in 2010, the software ecosystem on which it relied made several advances. By 2020 its paper 1 was being cited in peer-reviewed literature 4–5 times per week i. BoneJ became popular for bone morphometry, and in other fields such as materials, soil, and food science.

#IMAGEJ SOFTWARE REFERENCE ARCHIVE#

To enable other researchers to benefit from the development effort, plugins written by Doube and others were altered to suit the skeletal research domain (for example by using ASBMR standard histomorphometric nomenclature 6), bundled together in a single Java archive file ( BoneJ_.jar) for ease of installation, and basic user and developer documentation provided at. BoneJ was originally produced to satisfy a need to answer research questions using data to which extant software was ill-suited 3– 5. The plug-ins in BoneJ are intended for analysing computed tomographic (CT) and X-ray microtomography (XMT) images of whole bones, trabecular bone, and osteocyte lacunae. Java programs are executed inside an operating system-agnostic Java Runtime Environment (JRE). ImageJ plugins run on Windows, MacOS, GNU/Linux, and other operating systems because they are implemented in Java.

#IMAGEJ SOFTWARE REFERENCE CODE#

Both ImageJ and BoneJ are free and open-source, which means that their source code is readily available online for anyone to inspect, download, use, modify and distribute, taking an open science approach by providing all methodological details. For example, BoneJ provides a tool that counts connections within a structure by calculating an image’s Euler characteristic ( χ), a functionality that is absent from core ImageJ. A plugin is a piece of software that extends the capabilities of its parent application. See the authors' detailed response to the review by Mariana Kersh See the authors' detailed response to the review by Loic Courtois and Kamel MadiīoneJ 1 is a collection of bone image analysis plugins for the ImageJ 2 scientific image analysis software. Fixes a number of small typos in the text. Updates the user documentation URL to Updates the DOI (10.5281/zenodo.4635373) and version (styloid-r11) to the current ones. Note that this is a good example of how even minor variations in image processing parameters can affect readout values. This discrepancy is also present if the macro command setAutoThreshold is used in the scripting example, so it has been replaced with setThreshold(26892, 65535), which ensures the same threshold values are used in the scripting and interactive cases. There is a small difference in automatic threshold if the user clicks 'Auto' prior to clicking 'Apply' in the Threshold window, which results in a slight difference in BV and connectivity. Adjusts table of expected values to match those from following precisely the steps in the Interactive Use Case.

Fixes a typo and updates details to match new GUI elements in step 11 of the interactive use case.

Imagej software reference