RIKEN Center for Biosystems Dynamics Research, Laboratory for Morphogenetic Signaling (Hayashi Lab.)

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ImageJ Plugins

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ImageJ Plugins

Original ImageJ’s plugins have been developed to assist live imaging and image quantification. Please try them by downloading jar files from the following links and place in the ImageJ’s plugin folder of your computer.

*Please note that the plugins were checked in our working environment only (MacOSX, ImageJ java 1.8.0_60 build or later). If you notice any problem in the plugins please let us know. We will try to fix any problem you might encounter.

The user shall be responsible for any losses that may occur through the use of these plugins.

Oracle Java 8 License Changes Affect Plugins

As of July 4, 2019, the following plug-ins can not be started in Fiji for MacOS. This is because this plug-in uses JavaFX for the UI part. Some other plug-ins using JavaFX seem to be unusable.

Currently, Fiji and others have been built with AdoptJDK8 for MacOS due to the change of Oracle Java 8 license, but this does not include JavaFX. The Fiji developers seem to be thinking about moving to Java 11 in the future. This makes it possible to use JavaFX11, which is officially provided, and allows users to use JavaFX relatively easily. However, since it takes time to build with Java 11 (probably a code change is required), it seems to work in parallel to bundle JavaFX with AdoptJDK8. However, this also seems to be a difficult sign, and for the time being it seems to be an easy way to use in the previous version.

  • SplitViewCoordinator
  • ColorRangeExtractor
  • FRETratio
  • PeakConnectorFX
  • CrossSectionViewer

Downloadable list 

  • AutoCutB : Create an image(or stack) without background
  • AutoEnhance : Create a stack image that multiplies the ratio calculated from the average brightness of the first image
  • CoordinateShift : Align (auto and manual) the HyperStack image(registration) and Create the cross-section image
  • Original Lut files : Just LUT files
  • ColorRangeExtractor : Extract the image with set the range of color
  • FRETratio: Create the ratio image from 2 channel stack image
  • HSBprojector: Perform z-projection of ratio images while preserving the color meaning
  • CrossSectionViewer: Display the flexible cross section image by Line ROI
  • SaveMov : Create a mov(QuickTime) type of movie
  • SplitViewCoordinator : Create merged image from SplitView image
  • ZTinterpolation : Create a stack image expanded with the interpolated image
  • TPIV : Create a stack image processed by “Temporal” PIV
  • MovieLoader : Read a movie file
  • MovieToTiff : Convert movie to sequential tiff files without display
  • ReduceSpikeNoise : Remove the spike noise
  • ClippingArray : Create a Kymograph image using cropped image by rectangular ROI
  • CellDetection : Record and measure the ROI separated by the edge of the brightness such as the cell edge (automatic or manual)
  • SheetMeshProjection : A highly versatile ImageJ plug-in for extracting curved surfaces with arbitrary thickness and creating a image

Pending list

*There are broken links due to sequential release schedule

  • PeakConnectorFX
  • SegmentMeasure : Measure a part of the length of the selected ROI
  • SaveWebM : Create a WebM type of movie
  • ZRangeSelector : Create a Z-projected image with the Z axis range arbitrarily selected for each timepoint
  • ZahyoHyper : Record and measure the average brightness of the area where clicked the coordinates with the voluntary size ROI
  • LutSelector : Selectable panel for LUT

Tools