Homepage of Stephan Preibisch
PhD student in Tomancak Lab at Max Planck Institute of Molecular Cell Biology and Genetics in Dresden
ImageJ Plugins
Stitching 2D/3D
29/12/2008 6:50 pm
This is a plugin for fast stitching (translation only!)
of 2D and 3D images. It is based on Fourier Space analysis and offers very high speed
compared to plain cross correlation.
The 2D/3D Stitching Plugin is able to reconstruct big images/stacks from an arbitrary number of tiled input
images/stacks, making use of the Fourier Shift Theorem that computes all possible translations (x, y[, z])
between two 2D/3D images at once, yielding the best overlap in terms of the cross correlation measure. If more
than two input images/stacks are used the correct placement of all tiles is determined using a global
optimization. To remove brightness differences at the tile borders, a linear intensity blending is applied
You can find a complete HowTo for the plugins on the
Fiji project page.
If you have problems installing it, just download the whole
Fiji package, it is included there.
A FFT library from David Hale (Mines Java Toolkit)
is included as jar file. Just unzip the provided files into the ImageJ plugins directory.
For interactive examples have a look here.
Special thanks to Nicolas Gompel, James W. Truman, Simone Fietz and Wieland B. Huttner for providing the images.
Gaussian Convolution (2D/3D)
12/10/2007 3:07 pm
This is a plugin for performing a Gaussian Convolution on 2D and 3D images for arbitrary Sigmas (>0,5). You have several options for the assumption about the area outside the image which is needed to do a complete convolution. Simply uncompress the zip file into your plugins folder or do compile&run with the source. It is by the way multithreaded for 3D Gaussian Foldings. Just uncompress the zip file into your plugins folder and give it a try!
Download Binary ....
Download Source ....
FFT Transform Plugin (2D/3D)
20/02/2008 7:57 pm
This is a plugin for performing a (inverse) Fast Fourier Transform on 2D and 3D images. You can eigher compute the Power- and Phasespectrum for any image or compute the inverse transform for a given pair of the spectra. It is very fast thanks to the optimized 1D-FFT routines from David Hale which are included. For 3D FFT computations, the program is multithreaded. Just uncompress the zip file into your plugins folder and give it a try!
27/04/2008 7:22 pm
Fixed error in the rearranging of the quarters after computing the FFT.
Download Binary ....
Download Source ....
Principal Curvature Plugin (2D/3D)
20/02/2008 7:57 pm
This is a plugin for computing the Principal Curvatures of 2D and 3D images (not RGB). The Principal Curvatures can be computed for arbitrary structure sizes, which you can choose by perfoming a Gaussian Convolution first. For the Eigenvalue Decomposition I use the JAMA package which is included. Just uncompress the zip file into your plugins folder and give it a try!
Download Binary ....
Download Source ....
Sobel Filter Plugin (3D)
20/02/2008 7:57 pm
This plugin convolves a 3D image with a Sobel Filter. Just uncompress the zip file into your plugins folder and give it a try!
Download Binary ....
Download Source ....
Other software
The Hook Method for GeneChip Microarray Analysis
29/01/2008 2:02 pm
Calibration of microarray measurements aims at removing systematic biases from the probe-level data to get
expression estimates which linearly correlate with the transcript abundance in the studied samples. We address hybridization
on microarrays as a reaction process in a complex environment and express the measured intensities as a function of the input
quantities of the experiment.
The hook-method is a new calibration approach which is based on a graphical summary of the actual hybridization characteristics
of a particular microarray. The hook method provides a set of chip summary characteristics which evaluate the performance of
a given hybridization.
The algorithm of the method is briefly described and its performance is exemplified in this paper: PDF
Download Binary (16MB, with example files) ....
Download Short Installation Guide ....
Download Hook Paper ....