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KymoResliceWide

    Name

    KymoResliceWide

    Software

    ImageJ

    Author

    Eugene Katrukha and Laurie Young

    Maintainer

    Eugene Katrukha

    Source

    github

    Status

    stable

    Category

    Stacks

    This plugin builds kymographs using straight line, polyline or freehand selection of variable thickness (and using either average or maximum intensity across the line). So it is extended implementation of ImageJ’s Reslice function. Here are some thought on “Why another kymograph plugin?”.

    Using plugin

    Open the stack/movie to be analyzed in ImageJ. Draw a line along the area where you want to make a kymograph.
    You can use ImageJ’s native embedded characteristics of the line/curve, like:

    Line type

    Plugin automatically picks up your choice of line selection from ImageJ and corrects for its length.
    Just use the one you need.

    http://katpyxa.info/software/KymoResliceWide/line_selection2.png

    Line width

    Define the width of line using double click on the line selection tool in ImageJ

    http://katpyxa.info/software/KymoResliceWide/line_width2.png

    Parameters

    After that the window showing kymograph parameters will pop-up:

    http://katpyxa.info/software/KymoResliceWide/choice2.png

    Where following options are available (in order):

    • whether to take average or maximum intensity transverse to line;
    • (unchecked) time as y-axis, distance as x-axis, (checked) time as x-axis, distance as y-axis;
    • (checked) curve will be added and displayed in the overlay of original movie/stack to mark already analyzed region;
    • ignore original image/stack calibration, i.e. don’t add its calibration to the final kymograph image (width, height, vortex size and frame rate)

    Other kymograph plugins

    As alternative, there is very well documented Multi Kymograph plugin and its updated version Kymograph tool.

    Version history

    version 0.5 (2017/04/01): hyperstacks reslice fixed (now time, not Z) and image calibration handling is improved (with option to ignore it).

    version 0.4 (2015/10/21): now it works with hyperstacks and RGB images.