New windows: 3d Surface plot
Other New tools:
	image angle
	image distance
	color picker

----------

LUT: this should be a filter
	
image
	print

	info?
	crop
	set color depth

	draw
		pencil
		brush
		spray
		flood fill
		eraser

	Derive (analyze?)
		Histogram
		eigenvalues??
		statistics??
		3d+t color distribution plot

other new features:
	load movies mpg etc?
features that can be skipped?
	selection.fit spline
	selection.fit elipse
	selection.make band

	Jython, Ruby integration
	shadows?

!!
* somehow get out profiles, spatial and in time
* somehow list threads, used memory etc
* FRET calculator
* FRAP calculator
* auto-check for updates
* open recent: XML and OST

===============================================================================
     Filtered list of plugins worth converting/rewriting
===============================================================================
ImageJ Acquisition [top]
     Shading Corrector
     QuickTime Capture [Updated]
     TWAIN
     JTwain
     SensiCam Long Exposure Camera

     www.scioncorp.com: Scion Frame Grabbers and Firewire Cameras
     www.qimaging.com: QImaging Firewire Cameras
     ScionFGAkiz: Scion full-frame-rate capture
     FWCamAkiz: Mac OS X Firewire Cameras
     www.pixelsmart.com: PixelSmart Frame Grabbers
     www.bruxton.com: Andor, Cooke, Hamamatsu, PCO, Princeton Instruments,
        Photometrics, Red Shirt Imaging and SciMeasure Cameras
     www.aas2.com: Ann Arbor Sensor Systems AXT100
        Thermal Imaging Camera
     pco.orange8.ch: Cooke PCO, Sensicam and Pixelfly Cameras
     mbl.edu: CamAcqJ plugin for QImaging Retiga cameras (Windows only) [new]
     www.fclab.com: FCLab FC1000/2000 USB 2.0 Cameras (Windows only) [new]
     micro-manager.org (μManager)[new]: Open source; Zeiss and Nikon microscopes;
        Hamamatsu, Andor, PVCAM, DVC and IIDC Firewire cameras;
        Shutters, stages, etc by Vincent (Uniblitz), Ludl, Prior, ASI and Sutter
     xlimaging.us: XLi megapixel USB 2.0 cameras (Windows only) [new] 
===============================================================================

ImageJ Analysis [top]
     Autocorrelation
     MRI t2 calculations
     Line Analyzer
     Image Correlator
     Area Calculator
     Particle Remover
     Circularity
     Modulation Transfer Function
     Draw line or point grids [Updated]
     Moment Calculator
     Cell Counter
     Oval Profile Plot
     Color Comparison
     Radial Profile Plot
     MRI Analysis Calculator
     Sync Measure 3D
     Hough Circles
     Convex Hull, Circularity, Roundness
     Fractal Dimension and Lacunarity [Updated]
     Measure And Label
     Colocalization
     Granulometry
     Texture Analysis
     Cell Outliner
     Grid Cycloid Arc
     RGB Profiler
     Colocalization Finder
     Spectrum Extractor
     Contact Angle [Updated]
     RG2B Colocalization
     Color Profiler
     Hull and Circle
     MR Urography
     Template Matching
     Extract IMT from ultrasound images
     ITCN (Image-based Tool for Counting Nuclei)
     Multi Cell Outliner
     JACoP (Just Another Co-localization Plugin)
     CASA (Computer Assisted Sperm Analyzer)
     Radial Profile Plot Extended
     Concentric Circles (non-destructive overlay) [new]
     Azimuthal Average [new] 

===============================================================================

Collections [top]
     UCSD Confocal Microscopy Plugins
     MBF ImageJ for Microscopy Collection by Tony Collins [new]

===============================================================================

Color [top]
     RGB Stack Splitter
     RGB Stack Merge
     HSB Stack Splitter
     RGB Recolor
     LUT Lister
     Color Counter
     RGB Measure
     3D Color Inspector/Color Histogram
     RGB Measure Plus
     Color Space Converter [new]


===============================================================================

     Kuwahara Filter
     Auto Gamma (gamma correction)     

Filters [top]
     Background Subtraction and Normalization
     Kalman Filter
     Dual-Energy Algorithm
     Anisotropic Diffusion
     Mixture Modeling Thresholding
     Otsu Thresholding
     Maximum Entropy Thresholding
     2D Hybrid Median Filter
     3D Hybrid Median Filter
     Spectral Unmixing
     Haar Wavelet Filter and Adaptive Median Filter
     'A trous' Wavelet Filter
     MultiThresholder (Isodata, Entropy, Otsu, Mixture Modeling)
     Granulometric Filtering
     Windowed-Sinc Filter (low pass time series filter)
     Anisotropic Diffusion 2D (edge-preserving noise reduction)
     Linearize Gel Data
     Multi Otsu Threshold
     Spectral Unmixing of Bioluminescence Signals
     Lipschitz Filter //http://rsb.info.nih.gov/ij/plugins/lipschitz/
     

===============================================================================

Graphics [top]
     Reduce size using averaging
     Image Layering Toolbox
     Contour Plotter
     Dynamic Profiler
     Z-Axis Profiler
     Radial Grid
     Diffusion Limited Aggregate Models
     Fractal Growth Models

===============================================================================

Stacks [top]
     Object Tracker
     Stack Reverser
     Group_ZProjector
     Concatenator
     Stack Combiner
     Stack Histogram
     Stack Maker
     MultiTracker
     Time Stamper
     Stack Inserter
     Stack Normalizer
     Stack Focuser (extended depth of field)
     Substack Maker
     RGB Zprojector
     Concatenate Images or Stacks [Updated]

===============================================================================

Utilities [top]
     Straighten Curved Objects
     Combine Images to Create Mosaic
     Adjust Window and Level
     Joel Time Stamper
     Query DICOM Header
     Calculate Fura-2 (calcium) Ratios
     Stitch BLISS Tile Images
     Anaglyph (creates stereo images)
     Cairn Optosplit Image Splitter
     ROI Brush Tool

===============================================================================

More Sites with Plugins [top]
       VolumeJ, FlowJ, Flow3J, SurfaceJ, Register ROI,
       PCA (Principal Component Analysis)
       Active Contours (Snakes), Canny-Deriche Filter,
       Shape Analysis by Fourier Descriptors
       Surface roughness statistics, Dynamic threshold,
       Shape descriptors, Image correlation, Stack plots
       Expression (applies formulas to images), HPGL Reader, Warp,
       NTSC DV2Float, QuickTime Grab, Layers, Stack Sorter, Measure
       ROI, Polynomial Fit, PLOT3D I/O, Polar Gradient, 3D Fast Hartley
       Transform (FHT, FFT), 2D and 3D Deconvolution, Diffraction PSF 3D
       Fractal Count, Map Fractal Count, Susan Filtering,
       operators, dilation, erosion, 4- and 8-connected particle analysis
       color thresholding
       Align Stacks, Orthogonal Views (axial, coronal, and sagital)
       Clustering, Texture Synthesus, 3D Toolkit, Half-Median
       RGB to CIE L*a*b*, Multiband Sobel edges
       DCRaw (digital camera raw images), ImageJ for Zaurus PDA
       MultiTracker2, RGB Stack Merge2, ICS Opener, Optical Insights
       Running Z Projector, Binner, QED Swap
     TransformJ (Geometric Transformations up to 4D)
       Affine, Crop, Embed, Mirror, Rotate, Scale, Shift, Turn
     NeuronJ (Neurite Tracing and Quantification)
     ImageJ Documentation Wiki [new]
       Align_4, Align_RGB_planes, Align_Slice
       Fourier Shape Analysis
       Threshold_Colour, Colour_Deconvolution, Lut_Panel
       Canny-Deriche Edge Detection
       Morphological Operators, 3D binary morphological filters
       Active contour (Snake), LiveWire
       HyperVolume_Browser
       TrakEM2, Image5D, Thresholding by connection
       Cell Image Analyzer, IJUpdate, LSMToolbox, Action Bar
     TurboReg (image registration)
     Neuron Morphology
     Segmenting Assistant
     NucMed Collection (PET/SPECT imaging)
     Fractional Splines and Wavelets
     3D Editing
     Extended Depth of Field (in focus images from 3D objects) [Updated]
     Yawi3D (Yet Another Wand for ImageJ 3D)
     UnwarpJ (registration using warping)
     Find Colocalized Pixels in RGB Channels
     Measure Total Above Thresholded Area in a Stack
     StackReg (recursive alignment [registration] of stacks)
     Power and log transforms, contrast stretching, spatial filtering
     SpotTracker (particle tracking over noisy image sequences)
     Visible Human Preprocessing Toolkit
     DStretch (digital enhancement of pictographs) [new]
     SplineSnake (segmentation using active contour) [new]
     MIJ (interfacing ImageJ and Matlab) [new]
     DropSnake and LB_ADSA (contact angle measurement) [new]
     QA-Distri (plugins for QA in digital radiology) [new]
     bUnwarpJ (bidirectional elastic registration of images) [new]
     Scrollable StackWindow (mouse wheel support for stacks) [new]
     Open and z-project PerkinElmer Ultraview ERS RAW-files [new]
     ParticleTracker (particle detection and tracking from digital videos) [new]
     MTrackJ (track and analyze moving objects in image sequences) [new]
     Inhomogen Isotropic Diffusion 2D Filter [new]
     Introduction to Astronomical Image Processing using ImageJ [new]
     Chemotaxis and Migration Tool [new]
     RoiPushTool (edit area selections using circular brush) [new]
     SplineDeformationGenerator (cubic B-spline deformations) [new]
     Azimuthal Average [new]
