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IMACEL Partnership Approaches
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
- Copy the downloaded JAR file (lpx_ij_plugins_….jar) to the plugins folder of ImageJ.
- Start ImageJ or [Help -> Refresh Menus] if ImageJ is already running.
- LPX ImageJ plugins appered as [Plugins -> LPX -> …] .
Upgrade
- Delete old version of this plugins JAR file (lpx_ij_plugins_….jar) in the plugin folder of ImageJ.
- Copy the downloaded JAR file (lpx_ij_plugins_….jar) to the plugins folder of ImageJ.
- 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.