Search Results for "imagej"
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Showing 43 open source projects for "imagej"
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InteredgeDistance
An ImageJ macro to measure distance between two lines
InteredgeDistance is a macro for ImageJ/Fiji image analysis software. This tool measures the distance between two user-drawn lines on an image. For community help/support, please use https://forum.image.sc/. -
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Open Beam Profiler
Profiling and analysis of laser beams with ImageJ
This open-source software enables profiling and analysis of laser beams. It can be used with a variety of cameras supported by ImageJ and Micro-Manager, or images from any other source. It provides all common analysis methods like D4Sigma, knife-edge, as well as fitting of Hermite-Gauss, Laguerre-Gauss and super-Gauss functions. -
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TomoJ
ImageJ plugin to perform Electron Tomography
TomoJ is an ImageJ plug-in for tomographic reconstruction. It was designed for electron tomography, however any acquisition with parallel beam should work. TomoJ proposes the preprocessing and the registration of tilt-series prior to 3D reconstructions (WBP, ART, SIRT, OS-SART, compressed sensing). TomoJ is written in Java, the computations are multithreaded and reconstruction can be performed on CPU or GPU (OpenCL). -
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ADAMS
ADAMS is a workflow engine for building complex knowledge workflows.
...This allows rapid development and easy maintenance of large workflows, with hundreds or thousands of operators. Operators include machine learning (WEKA, MOA, MEKA) and image processing (ImageJ, JAI, BoofCV, LIRE and Gnuplot). R available using Rserve. WEKA webservice allows other frameworks to use WEKA models. Fast prototyping with Groovy and Jython. Read/write support for various databases and spreadsheet applications. -
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FijiWings for Mac and Windows
automated fly wing analysis
Overview: Here we present FijiWings for Mac and Windows, a set of macros designed to perform semi-automated morphophometric analysis of a wing photomicrograph. FijiWings uses plug-ins installed in the Fiji version of ImageJ to rapidly and accurately measure wing area, reliably detect trichome positions and calculate trichome density of a wing region selected by the user. UPDATES: 12-6-20 Fijiwings 2.4 for Mac is uploaded. Bundles JAVA and ImageJ update to the current day. Following download, runs on a Imac and a MacBook running Mojave and Catalina. ... -
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These are plugins to Fiji (ImageJ) originally developed at Nuclear Medicine at Beth Israel, Boston MA. Pet_Ct_Viewer is for PET/SPECT - CT/MRI studies showing fusion of the modalities. Read_BI_Studies is for BI database activities. See http://petctviewer.org
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SEM3De
ImageJ plugin to enhance stack of images acquired by SEM
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FijiwingsPolarity
A tool to detect trichome polarity in the fly wing
Tools allow the detection of trichome polarity and direction rendered as (a) an arrow (black/white or color based on 360 degree direction) or (b) heat map of overlay. Files for download include (1) Fiji (Fiji Is Just ImageJ) package (.tar file) suitable for download (with and without Java Run Time) and (2) example images suitable for testing these tools. Further description to follow. -
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PhysImage
A fork of ImageJ that adds useful functionality for physiologists
PhysImage is a fork of the popular ImageJ software that adds functionality for physiologists, specifically of the electrophysiologist flavor, to more easily integrate imaging and electrophysiological data together for analyses/display and also for the automation of these analyses/display operations during experiments. -
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FATCALC-ImageJ is an ImageJ macro (fully automated) for unsupervised fat segmentation in magnetic resonance imaging. It was developed for GE T1 2-points Dixon sequences (fat only image). FATCALC independently evaluates the volumes of visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT).
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The automatic quantification of foci on fluorescent images of cells after DNA damage is widely used for estimation of the DNA double-strand break number in DNA of single cells. We present a graphical user interface FoCo, which was developed in Matlab together with ImageJ for individual foci count using image analysis.
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SMlocalizer
CUDA based ImageJ plugin for single molecule localization microscopy
SMLocalizer is a CUDA enabled ImageJ plugin for single molecule localization microscopy. The plugin aims to be a user friendly and powerful alternative to currently availible softwares where most settings are iteratively obtained by the software, not the user. The current version handles 3D multichannel data in any format that can be loaded into ImageJ/ Fiji. 3D modalities supported are PRILM, Biplane, Double helix and astigmatism. -
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NRRD Image Library for C++
Header Only C++ Library to read and write NRRD image files
...It implements "the most important" parts of the following standard: http://teem.sourceforge.net/nrrd/format.html - Does not implement: line skip, byte skip, orientations, encodings other than raw, kinds other than domain. - Converts all type strings to C-type equivalent i.e. "uint8" to "unsigned char" - Always writes "endian" tag (required for FIJI/ImageJ loading) - Can open files of Big and little endian but saves files only in native format. It is compatible with ImageJ/Fiji http://fiji.sc/Fiji The library has been used in dozens of projects and is well tested. -
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clockscan
It is the Project for develop an ImageJ plugin
This plugin is used to measure the intensity of the brightness of the image of the radial scan profiles in the region of interest (ROI). Install the latest versions of bundled Java and either ImageJ or Fiji ImageJ as recommended on the respective websites, https://imagej.nih.gov/ij/ and https://fiji.sc/. In the text below, both programs will be referred to as “ImageJ”. Copy “Clock_Scan-1.0.1.jar” and “Multi_Clock_Scan-1.0.1.jar” or "Clock_Scan_combined-1.0.1.jar" and paste them into the ImageJ plugin directory. -
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WrapImaJ
Multi-platform API for Image Processing systems in Life Sciences
...The purpose of WrapImaJ is not to combine an exhaustive collection of all functionalities of different imaging system, but to offer a simple, concise Application Programming Interface (API) - allowing to develop imaging software, the source code of which is independent from the underlying imaging system on which it relies. In it's current form, it only wraps basic functionalities of ImageJ. The developers of WrapImaJ intend the library to support compatibilty with the main imaging systems available in the Java language and broadly used in the field of life sciences. -
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SmartRoot
Semi-automated root image analysis software
...The software supports a sampling-based analysis of root system images, in which detailed information is collected on a limited number of roots selected by the user according to specific research requirements. SmartRoot is an operating system independent freeware based on ImageJ and uses cross-platform standards (XML, SQL, Java) for communication with data analysis softwares. To cite us: Guillaume Lobet, Loïc Pagès and Xavier Draye. A Novel Image Analysis Toolbox Enabling Quantitative Analysis of Root System Architecture. 2011 Plant Physiology, Vol. 157 -
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The 'ImageJ Plugins' project is a source of custom plugins for the Image/J software. Image/J is a public domain image processing and analysis program developed in Java (http://rsb.info.nih.gov/ij/).
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ImageJ AIOT
An addon for ImageJ allowing the measurement of acetabular cups
ImageJ acetabular implant orientation tool (AIOT) is an addon for ImageJ that allows the measurement of the inclination and version of prosthetic acetabular cups from plain film pelvic Xrays. This uses the fitted ellipse method first described by Lewinnek in 1978. It is suitable for use on a wide variety of total hip replacements -
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ImagingBook
Java source code for image processing books by Burger & Burge
NOTE: The source repository for this project has been moved to a NEW LOCATION: ************************************************************************************ https://github.com/imagingbook/imagingbook-public ************************************************************************************ -
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Cell Colony Edge
Cell Colony Edge ImageJ macro and CellProfiler pipelines
This gives the Cell Colony Edge ImageJ macro, and the CellProfiler pipelines used in the paper. This also provides the images used in the paper. -
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Cell Sampler
Cell Sampling Plugin for ImageJ
Cell-Sampler is an ImageJ sampling plugin written in Java. It is designed to extract time series from microscopy images of oscillating cells expressing the GFP or Luciferase reporter molecule. This program was developed in the Piggin's Laboratory at the University of Manchester. Go to the Cell-Sampler Web Site for installation instructions and tutorial materials. -
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Phanto_maJ
build three dimensional structure
PhantomaJ is a software which aims to help users designing complexe three dimensional structures and building phantom banks. This software, implemented as an ImageJ plug-in, has been designed to be intuitive. PhantomaJ is thus "ready to use" for most users, but advanced users can choose to modify specific parameters such as intersection mode, intensity decrease function or virtual real three dimension. In addition, adding a new "basic form" consiste for advanced users to write two short java file ( one describing the new form geometry and the other transcripting this geometry in java3D world ). ... -
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iSBatch
Hyearchical Data Processing Plugin for ImageJ
iSBatch is a Java-based plugin for ImageJ (version 1.49d) or its distribution Fiji. iSBatch is designed for quick evaluation of analysis pipelines and visual exploration of datasets. It is distributed under an open open-source license (GNU General Public License, version 3). The plugin handles the data in a hierarchical fashion based on a source folder containing all data and little guidance provided by the user. -
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ijTools
A set of plugins and tools for ImageJ (Image processing sofware)
A collection of plugins and tools for the ImageJ software. Contains modules for image filtering (directional filtering), segmentation, analysis (perimeter estimation, geodesic diameter...), or visualisation (image overlay).
