ImageJ plugins

ImageJ is an image Processing and analysis application written in Java by Wayne Rasband. It is free and it's source code is available, making it an extremely atractive platform for development of new image analysis tools. Here, you'll find ImageJ plugins developed at the Vale lab at UCSF.

Plugin Brief Explanation
MTrack2 Tracks multiple objects in a stack. Based on the Multitracker plugin, but can deal with appearing and disappearing objects. 9/22/03: Added calculation of total distance traveled. 07/03/08: Now can input variables from a plugin.
GaussianFit Fast Gaussian fitting plugin. Works both as a Micro-Manager and an ImageJ plugin. Can track single particles or fit all spots in image series.
Ics_Opener Opens Files saved in ics/ids format. 5/19/04: Added error checking by Wayne Rasband. 7/11/08: This plugin will no longer be supported. Please use the LOCI Bio-Formats plugin instead.
IC100BMP_Reader Opens 8 and 16 bit BMP files from the Beckman IC100. 16 bit BMPs (a non-standard file format) are not opened by the standard File Open command in ImageJ. Use this plugin instead.
IxMicro_Opener Reads in time-series acquired with the IxMicro into stacks in ImageJ. Use the macro drawBoxAndSave_.txt to make selections from the opened images.
FolderWithStacks_to_Movie Assembles all stacks in a folder (should all have same x and y dimensions) into a single stack.
OI_crop Optical Insights makes a device that projects two colors on the right and left hand side of the camera. This plugin crops both the left and rights side of the image.
OI_measure This plugin measures the intensity in a box of user-defined size in the left and right half of an image
OI_cut_RGBmerge This plugin cuts image stack made with the Optical Insights device into two image stacks, and combines them into an rgb image stack.
Running_ZProjector Makes a 'running average' from a stack. Useful to increase the signal-noise ratio in video-sequences at the cost of temporal resolution
Binner Binner reduces the size of an image or stack by binning groups of pixels of user-specified sizes. The resulting pixel can be calculated as average, median, maximum, or minimum. As of ImageJ 1.46i, this functionality is included with ImageJ (Image>Transform>Bin)
QED_swap TIFF sequences saved by QED are not always imported correctly by ImageJ. This plugin renames the files such that they will be imported in the correct sequence.
GridAligner When acquiring images with 2 cameras simultanuosulty, it is difficult to perfectly align the images. This plugin will perform an affine transform on the second channel of a multi-channel image, based on an affine transform that is determined by imaging difraction limited spots onto both channels simultanuously. Once calibrated, the transform can be applied on many experimental images.

All plugins including source code are bundled in: Simply download this file to your plugins folder, unzip the contents ('unzip IJPluginsvl.z', use Stuffit on Mac OS 8/9) into the ImageJ plugin folder, and restart ImageJ. Ics_Opener is placed in 'InputOutput', Running_ZProjector and the OI plugins in 'Stacks', and QED_swap in 'Utilities'. You can also download the tar.gz version if you prefer. By downloading this software you agree with the terms of the license.

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