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One of Fiji's principal aims is to make the installation of ImageJ, Java, Java 3D, the plugins, and further convenient components, as easy as possible. As a consequence, Fiji enjoys more and more active users.
ImageJ is a Java-based image processing program developed at the National Institutes of Health and the Laboratory for Optical and Computational Instrumentation (LOCI, University of Wisconsin). [ 2 ] [ 3 ] Its first version, ImageJ 1.x, is developed in the public domain , while ImageJ2 and the related projects SciJava , ImgLib2 , and SCIFIO are ...
Pre-trained workflows can be executed directly from ImageJ/Fiji using the ilastik-ImageJ plugin. [4] Pre-trained ilastik Pixel Classification workflows can be run directly in Python with the ilastik Python package, [5] which is available via conda.
Simple interactive object extraction (SIOX) is an algorithm for extracting foreground objects from color images and videos with very little user interaction. [1] It has been implemented as "foreground selection" tool in the GIMP (since version 2.3.3), as part of the tracer tool in Inkscape (since 0.44pre3), and as function in ImageJ and Fiji (plug-in).
This limits how much of ImageJ can be changed without breaking backwards-compatibility, which has caused design flaws to accumulate over time. Endrov sacrifices all backwards-compatibility for a clean design. While ImageJ consists of a core and rather independent plugins, Endrov has few core functions and plenty of plugin-plugin dependencies.
IMOD includes over 180 command line programs listed here and three main GUI programs: . 3dmod - IMOD's main GUI used to view and segment images and 3D vector models.; Midas - A program used to align images over the top of each other, typically to apply fine adjustments after automatic cross-correlation.
Endrov – Java-based plugin architecture designed to analyse complex spatio-temporal image data; Fiji – ImageJ-based image processing; Ilastik – Image-classification and segmentation software; ImageJ – Image processing application developed at the National Institutes of Health; IMOD – 2D and 3D analysis of electron microscopy data
ClearVolume [1] is an open source real-time live 3D visualization library designed for high-end volumetric light sheet microscopes.ClearVolume enables the live visualization of microscope data - allowing the biologists to immediately decide whether a sample is worth imaging.