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
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- Clustering
- plugins for clustering ( k-means, mean-shift, SOM, spectral clustering, etc.)
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- Color
- plugins for color space conversion, color histograms, convert greyscale
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- Convolv
- plugins for convolution for 2D or 3D images
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- CorrMap
- plugins for correlation diagram for images or frames
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- Correspond
- plugins to estimate congruent points between 2D-images
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- DispRange
- plugins for automatic contrast-brightness control
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- DynProf
- plugins to make kymograph, luminance distribution, luminance histogram
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- Features
- plugins for feature extraction from 2D-gray-scale images and its ROI
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- Filter1d
- plugins for image processing to 1D table coordinate
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- Filter2d
- plugins for image processing to 2D images (antinoise measures, binarization, etc. )
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- FilterPt
- plugins for image processing to each pixels ( time-gamma curve, etc.)
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- Flow
- plugins for optical flow to sequential grey scale image
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- IjTool
- plugins for each project
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- LinesAngle
- plugins quantify length of line, angle, etc.
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- Measure
- plugins for shape measurement to blobs in 2D images
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- Pad
- plugins for padding process to 2D or 3D images
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- Peak
- plugins to extract brightness peak from 2D gray scale images
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- Ptv
- plugins for the processing speed from particle‐tracking
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- RangeEffect
- plugins for image processing in a parameter range
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- Registration
- plugins for images registration
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- RoiUtil
- plugins for image processing to ROI
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- Stics
- plugins for image processing to spatial-temporal image correlation spectrum
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- StkFilter
- plugins for image processing to stack images ( xyz or time series)
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- 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
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- 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.
