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Software package as distribution of ImageJ and ImageJ2 together with Java, Java3D and plugins organized into coherent menu structure. Used to assist research in life sciences.
Proper citation: Fiji (RRID:SCR_002285) Copy
Software toolkit for analyzing tool for microscopic images. It contains plugins and some macros dealing with image filtering, image segmentation and binary image processing and analysis.
Proper citation: BioVoxxel Toolbox (RRID:SCR_015825) Copy
http://www.nanotomy.org/OA/Sjollema2016MI/
ImageJ macro to detect, mark and count electron dense markers like goldgrains or quantum dots in electron micrographs.
Proper citation: Golddigger (RRID:SCR_020960) Copy
https://github.com/howisonlab/softcite-dataset
Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale.
Proper citation: SoftCite (RRID:SCR_024411) Copy
Debian is Linux distribution composed of free and open source software, developed by community supported Debian Project, which was established by Ian Murdock on August 16, 1993.Debian comes with over 59000 packages (precompiled software that is bundled up in nice format for easy installation on your machine), package manager (APT), and other utilities that make it possible to manage thousands of packages on thousands of computers as easily as installing single application.
Proper citation: Debian (RRID:SCR_006638) Copy
Software tool to measure area of invading spheroid in 3D cell invasion assay. Can also count and measure area of nuclei within spheroid.
Proper citation: Analyze Spheroid Cell Invasion In 3D Matrix (RRID:SCR_021204) Copy
https://imagej.net/plugins/sholl-analysis
Open source program for ImageJ/Fiji. Automated and multithreaded Sholl for direct analysis of fluorescent images and/or traced morphologies. Features quantifications based on curve fitting. Analysis of profiles obtained by other software is also possible.
Proper citation: Sholl Analysis (RRID:SCR_022758) Copy
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