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While Fiji was originally intended for neuroscientists (and continues to be so [8]), it accumulated enough functionality to attract scientists from a variety of fields, such as cell biology, [9] parasitology, [10] genetics, life sciences in general, materials science, etc. As stated on the official website, the primary focus is "life sciences ...
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 ...
There are several packages that make bioimage informatics methods available through a graphical user interface such as ImageJ, FIJI, CellProfiler, chunkflow or Icy. Visualization and analysis platforms such as Vaa3D have appeared in recent years and have been used in both large scale projects especially for neuroscience and desktop applications.
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.
[10] CellProfiler interfaces with the high-performance scientific libraries NumPy and SciPy for many mathematical operations, the Open Microscopy Environment [ 11 ] Consortium’s Bio-Formats library for reading more than 100 image file formats, ImageJ for use of plugins and macros, and ilastik for pixel-based classification. [ 12 ]
Learn how to download and install or uninstall the Desktop Gold software and if your computer meets the system requirements.
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.
Functional MRI FABBER FABBER is a Bayesian model fitting tool intended for use in task modelling of ASL data.: FEAT Model-based FMRI analysis with straightforward but powerful GUI: data preprocessing (including slice timing correction, MCFLIRT motion correction and PRELUDE+FUGUE EPI unwarping); FILM GLM timeseries analysis with prewhitening; registration to structural and/or standard space ...