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

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ImageJ Plugins

3D image surface projection

A highly versatile ImageJ plug-in for extracting curved surfaces with arbitrary thickness and creating a image

Extraction that ignores fine irregularities is possible by using a coarse mesh

Source code : https://github.com/Wada-H/SheetMeshProjection

Package file

  • SheetMeshProjection_.jar
  • CrossSectionViewer_.jar
  • SampleData-HypocotylComposite.tif, roidata1
  • manual-Japanese.txt
  • manual-English.txt

*The image used for sampleData is a slightly modified version of the image used in the following paper.

Erguvan Özer, & Verger Stéphane. (2019). Dataset of confocal microscopy stacks from plant samples – ImageJ SurfCut: a user-friendly, high-throughput pipeline for extracting cell contours from 3D confocal stacks [Data set]. Zenodo. http://doi.org/10.5281/zenodo.2577053

How to install:

ImageJ

Fiji

  • Add the following site to “Manage update sites” of ImageJ Updater(Help > Update…)
  • https://sites.imagej.net/SheetMeshProjection/
update-siteのリスト画像

Sample Movie:

Sample Movie 1 (386MB)

Update log:

~Update ver. 1.0-20200824 ~

  • Add Priority function

~ Add the update site on Fiji 20200717~

  • Partially modified according to Interractive_3D_Surface_Plot-3.0.0

~ Update ver. 1.0-20200629 ~

  • Supports single channel image
  • Improved to synchronize the colors of XZ and YZ images with the main image

~ Released ver. 1.0-20200528 ~