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LPIXEL ImageJ Plugins

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With dependent libraries

Recommendations for most ImageJ users.

Without dependent libraries

 

Scala runtime library should be installed.
Following libraries are used in LPIXEL ImageJ Plugins.

Analyze Menu

  • Clustering
    plugins for clustering ( k-means, mean-shift, SOM, spectral clustering, etc.)
  • Color
    plugins for color space conversion, color histograms, convert greyscale
  • Convolv
    plugins for convolution for 2D or 3D images
  • CorrMap
    plugins for correlation diagram for images or frames
  • Correspond
    plugins to estimate congruent points between 2D-images
  • DispRange
    plugins for automatic contrast-brightness control
  • DynProf
    plugins to make kymograph, luminance distribution, luminance histogram
  • Features
    plugins for feature extraction from 2D-gray-scale images and its ROI
  • Filter1d
    plugins for image processing to 1D table coordinate
  • Filter2d
    plugins for image processing to 2D images (antinoise measures, binarization, etc. )
  • FilterPt
    plugins for image processing to each pixels ( time-gamma curve, etc.)
  • Flow
    plugins for optical flow to sequential grey scale image
  • IjTool
    plugins for each project
  • LinesAngle
    plugins quantify length of line, angle, etc.
  • Measure
    plugins for shape measurement to blobs in 2D images
  • Pad
    plugins for padding process to 2D or 3D images
  • Peak
    plugins to extract brightness peak from 2D gray scale images
  • Ptv
    plugins for the processing speed from particle‐tracking
  • RangeEffect
    plugins for image processing in a parameter range
  • Registration
    plugins for images registration
  • RoiUtil
    plugins for image processing to ROI
  • Stics
    plugins for image processing to spatial-temporal image correlation spectrum
  • StkFilter
    plugins for image processing to stack images ( xyz or time series)
  • SwapAxis
    plugins for swapping x-y-z axis in a image
Supported System
・ImageJ 1.48 or later http://rsbweb.nih.gov/ij/download.html
・Fiji: http://fiji.sc/Fiji
Installation
1.Copy the downloaded JAR file (lpx_ij_plugins_….jar) to the plugins folder of ImageJ.
2.Start ImageJ or [Help -> Refresh Menus] if ImageJ is already running.
3.LPX ImageJ plugins appered as [Plugins -> LPX -> …] .
Upgrade
1.Delete old version of this plugins JAR file (lpx_ij_plugins_….jar) in the plugin folder of ImageJ.
2.Copy the downloaded JAR file (lpx_ij_plugins_….jar) to the plugins folder of ImageJ.
3.LPX ImageJ plugins appeared as [Plugins -> LPX -> …]
Author
Natsumaro Kutsuna (LPIXEL Inc., Hasezawa Lab in Univ of Tokyo)
References of each plugins
Plugins
・Lpx Filter2d -> filter=lineFilters__ -> lineMode=lineByMdnms__ (Sun and Vallotton 2009)
・Lpx Filter2d -> filter=lineFilters__ -> lineMode=lineByRotWs__ (Chiba et al. 2014, Kimori et al. 2010)
・Lpx Filter2d -> filter=lineFilters__ -> lineMode=lineExtract__ (Ueda et al. 2010)
・Lpx Filter2d -> filter=morpho__ -> morphoOp=rmp* (Kimori et al. 2010)
・Lpx Flow (Ueda et al. 2010)
References
・Chiba K, Shimada Y, Kinjo M, Suzuki T, Uchida S (2014) Traffic 15: 1-11.
・Kimori Y, Baba N, Morone N (2010) BMC Bioinfo 11: 373.
・Ueda H, Yokota E, Kutsuna N, Shimada T, Tamura K, Shimmen T, Hasezawa S, Dolja VV, Hara- Nishimura I (2010) Proc Natl Acad Sci USA 107: 6984-6899.
・Sun C, Vallotton P (2009) J Microsc 234: 147-157.
Acknowledgement
・Revision 76 (2007-09-18) – 882 (2010-10-03) had been supported by BIRD of Japan Science and Technology Agency (JST).
・Revision 883 (2010-10-03) – 1306 (2014-03-29) have been supported by `Development of Systems and Technology for Advanced Measurement and Analysis of Japan Science and Technology Agency (JST)
・Revision 1057 (2012-04-20) – 1383 (2015-03-31) have been supported by JSPS KAKENHI (No. 24770038).
・Revision 1194 (2013-05-09) – 1383 (2015-03-31) have been supported by a Grant-in-Aid for Scientific Research on Innovative Areas (No. 23119505) from the Ministry of Education, Culture, Sports, Science and Technology of Japan.

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