Search Results for "fiji"
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Showing 16 open source projects for "fiji"
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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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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... -
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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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FIJI ForthIsh Java Interpreter
Java interpreter with Forth-like syntax, use it for testing java libs
FIJI the ForthIsh Java Interpreter is an interactive environment with a procedural syntax similar to the Forth programming language. FIJI can load, introspect, and execute Java classes and methods. FIJI's main use is for unit and component testing of Java. -
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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... -
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MORPHEUS for Fiji
A tool for unbiased and reproducible cell morphometry in Fiji/ImageJ2
MORPHEUS is a Fiji/ImageJ2 plugin for the automated evaluation of cell morphometry from cell cultures images acquired by fluorescence microscopy. Specifically, MORPHEUS works with sampling distributions to learn—in an unsupervised manner and by a non-parametric approach—how to recognize the cells suitable for subsequent analysis. Afterwards, the algorithm performs the evaluation of the most relevant cell-shape descriptors over the full set of detected cells. Optionally, also the extraction... -
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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
... 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. -
Discover and manage administrator, service, and web app passwords, keys, and identities. Automate management with approval workflows. Centrally control, audit, monitor, and record all access to critical IT assets.
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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... -
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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. The software is designed for rapid exploration of large datasets... -
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Multiview Lightsheet Data Reconstruction
Software for the reconstruction of multiview microscopic acquisitions
..., and/or deconvolved. Standard confocal data is also supported. A detailed video tutorial: https://www.youtube.com/watch?v=0IkaSwfPYw0 Developers webpage: http://www.preibisch.net The software is distributed as Fiji plugin (http://fiji.sc/) using the Fiji Updater, just add the BigDataViewer Update Site. Source code is also available on GitHub (https://github.com/fiji/SPIM_Registration). Any issues, comments & feature requests can be discussed here. Documentation is available on the Fiji Wiki: -
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Airway Morphology for FIJI
FIJI App for Quantifying Airway Morphology
Run with FIJI make sure you have Fiji, AnalyzeSkeleton, Skeletonize3D, ImageViewer download .jar file into plugins folder, restart FIJI Input takes two 3D images (image stacks) 1.) Volume 2.) Skeleton representation of the volume. Output. Various airway morphometrics (eg. diameter, length), also tesselated 3D models -
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2P Toolbox
Two-Photon Data Analysis Toolbox
The 2P_Tools.jar is a series of hopefully useful Fiji Plugins to evaluate data acquired by two-photon imaging. It supports multiple features like conversion to normalized image stacks, preprocessing and image segmentation. -
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im-browser
MIB is a high-performance software package for image segmentation
Microscopy Image Browser (MIB) is a high-performance software package for advanced image processing, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets. Home page: http://mib.helsinki.fi
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