to the plugins folder, restart ImageJ, and there will be a new “Hybrid Median Filter” command in the Plugins menu.
This plugin consists of a 3D adaptation of the Hybrid Median Filter intended for XYZ or XYT data,
which we are calling a 3d Hybrid Median Filter. In this implementation, the median
is calculated from the medians of 1) the 3×3 2d PLUS kernel, 2) the 3×3 2d X kernel,
3) the 3×3 3d PLUS kernel, and four 3×3 2d X kernels through the center pixel along
Z-axis: 4) the vertical X, 5) the horizontal X, 6) the X from the upper right to the
lower left, and 7) the X from the upper left to the lower right, and optionally
8) the pixel in question. The 3D median model is experimental, intended for series
(time or finely-spaced z slices) where high noise places little confidence on individual
pixel values per image. The pixel in question receives less weighing in medians (included
in 7 medians calculations) versus checked (7 median ranks plus median of the 7 AND the
pixel). Checking the box retains single pixel data more (see frame numbers or 1-pixel
scratches), and performs less data “restoration”. Since the filter samples local
3x3x3 volumes, data stacks should be oversampled. The top and bottom edge pixels
are reflected outward, and the side edge pixels are wrapped arpund to complete the edge bound kernels.
The pixels of the first and last slice are reflected outward to simulate data for the N-1
and N+1 slices (where N is the number of images in the stack) in order to return an output
stack which is the same size as the input stack. The filter may be aborted by hitting the escape key.See 2d Hybrid Median Filter for a version which works on single images
and slices of a stack independent of one another.
Copyright (C) 2004 CHRISTOPHER PHILIP MAUER and VYTAS BINDOKAS
Permission to use, copy, modify, and distribute this software for any purpose
without fee is hereby granted, provided that this entire notice is included in
all copies of any software which is or includes a copy or modification of this
software and in all copies of the supporting documentation for such software.
Any for profit use of this software is expressly forbidden without first
obtaining the explicit consent of the author.
THIS SOFTWARE IS BEING PROVIDED “AS IS”, WITHOUT ANY EXPRESS OR IMPLIED WARRANTY.
IN PARTICULAR, THE AUTHOR DOES NOT MAKE ANY REPRESENTATION OR WARRANTY
OF ANY KIND CONCERNING THE MERCHANTABILITY OF THIS SOFTWARE OR ITS FITNESS FOR ANY
The plugin operates on a previously opened stack of images, and
produces a new stack of filtered images. The output stack is
generated upon completion of processing for all of the input data. Be sure to save
the output if desired.
Figure 1) 3d Hybrid Median Filter Demo
The lefthand frame represents the original data, the middle is filtered data excluding the
pixel in question in the final median (unchecked option), and the righthand side is the filtered data
including the pixel in question (checked option). Playback on key frames is slowed to allow
appreciation of intended effects and event description.
This aniGif is a high speed, low light stream of Fluo-4 in chick cardiomyocytes
using a CARV spinning disk confocal and an EMCDD camera.
Credits MW Roe and P Schumacker UofC.
Author: Werner Bailer (firstname.lastname@example.org) Date: 2001/10/29 Source: DCT_.java Installation: Download DCT_.class and DCT.class to the plugins folder and restart ImageJ. Description: Calculates forward and inverse