Search Results for "imagej"
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Showing 63 open source projects for "imagej"
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Image Tensors
Convert Lif, Czi, Metamorph ND, Oib to TIFF with ImageJ compatibility.
...It benefits researchers and scientists requiring efficient image format conversion. Key Features: Support for Multiple Formats: Converts Lif, Czi, Metamorph ND, and Oib. Uniform TIFF Output: Ensures compatibility with ImageJ. User-Friendly Interface: Simple command-line interaction. Batch Processing: Handles multiple files within a directory. Customizable Settings: Allows specifying output directory and file naming. ImageJ Compatibility: Ensures TIFF files are compatible with ImageJ. Usage: Single File Conversion: Input path to a single image file. ... -
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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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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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Foci quantitation
ImageJ script to characterise fluorescent foci.
This set of tools to allow high-throughput quantitation of foci fluorescence levels. The script was designed to work with 3D images of tagged kinetochore proteins in yeast. -
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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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The application Bio7 is an integrated development environment for ecological modelling and contains powerful tools for model creation, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.
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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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Ginkofast
ImageJ Macro to measure the fluorescence of an object in one timeframe
ImageJ Macro to measure the fluorescence of an object in one timeframe -
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ViralCounter
Simple macro to automatically count plaques in each well
A macro for ImageJ that simplifies detection of wells and counts viral plaques in each well. Try playing with the parameters to find the best results. If you need help send me a message. If you think my work is useful you can buy me a coffee! https://www.buymeacoffee.com/mcacciabue -
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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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ANDTool
Analysis Nuclei DAB (AND) Tool
Analysis Nuclei DAB (AND) Tool is a Graphical User Interface (GUI) to analyse microscopy images representing cells with nuclei stained using DAB dyes. The tool requires as input the original RGB images, and the FastRed, FastBlue, DAB channel, easily obtained using the Fiji function: "ImageJ" -> "Image" -> "Colour Deconvolution" -> "FastRed FastBlue DAB" Then, the tool first segment the nuclei using the FastBlue channel and the DAB channel, and then computes statistics by subdividing the sample in three regions according to the FastRed channel: a dark-red ROI, a light-pink ROI and a white ROI. ANDTool is written in MATLAB (The MathWorks, Inc., Massachusetts, USA) and the source code and standalone versions are here available for download. ... -
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ViralPlaque
A fast, open-source and versatile ImageJ macro for the automated dete
Plaque assay has been used for a long time to determine infectious titers. We present ViralPlaque, a fast, open-source and versatile ImageJ macro for the automated determination of viral plaque dimensions from digital images. Also, a machine learning plugin is integrated in the analysis algorithm for adaptation of ViralPlaque to the user’s needs and experimental conditions. A high correlation between manual and automated measurements of plaque dimensions was demonstrated. -
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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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Undistorter
Lens radial distortion correction - ImageJ plugin
This ImageJ plugin uses the division model proposed by Bukhari, F.; Dailey, M. N. (2013) to undistort images. The user can manually set the parameters k1, k2, and k3. The user can also draw segmented lines. After, by clicking on the Optimize button, the software will attempt to undistort the image transforming the segmented lines into straight lines. -
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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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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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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/).