From Endrov and VWB

Contents 1 Basic 2 Data formats 3 Movie formats 4 Data Type Extensions 5 Processing 6 Image processing 7 Image Processing (old filters, all deprecated, pending rewrite)

Basic

For the user:

• Image Window
• Model Window
• Console Window
• Plugin Window
• Keybinding
• Hardware
• Recording

Low level:

• Plugin BasicWindow
• Plugin EV
• Plugin MacBinding
• Plugin Imageset
• Plugin Data

Data formats

• OST
• LOCI Bio-Formats
• Acetree
• Basic imagesets importer
• OME integration - image database
• ImServ - OST database

Movie formats

• Plugin MovieOutputFFMPEG
• Plugin MovieOutputImageSeries
• Plugin MacBinding

Data Type Extensions

• Nucleus Lineage, Lineage Window
• Frame/Time
• Shell
• Image annotation
• Lines
• ChromaCount stats KJ
• Custom data

Processing

• Make QuickTime Movies

Image processing

• Particle measure

Image Processing (old filters, all deprecated, pending rewrite)

These plugins are indexed by position in filter menu. Not all filters below are completed yet.

Enhance: Contrast & Brightness, Histogram equalize, Sharpen 2D, Deinterlace, Confocal X Shift, low-pass filter, high-pass filter, butterworth filter, custom linear filter, median filter, IJ smooth, IJ sharpen, IJ enhance contrast

Mathematical: Convolve 2D, Gaussian 2D, Laplacian of Gaussian (LoG) 2D, Windowed Mean 2D, MaxZ, SumZ, Add, Threshold, Gradient, Laplacian, Hessian, Canny, IJ find edges

Noise: Binomial, Exponential, Gamma, Gaussian, Poisson, Salt and Pepper, Uniform

Transforms: FFT, FFT^-1, Invert, Radon, Radon^-1, DCT, DCT^-1, Convolve, Deconvolve

Binary Morphology: Erode, Dilate, Close, Open, Outline, Skeletonize, Fill holes, Make distance map

Order Statistics: Median filter, Max filter, Min filter, order filter

Other: