Video Microscopy Analysis
com.srbenoit.microscopy
This package provides a filter set to support analysis of sets of images gathered through video fluorescence microscopy.
- This package contains support subpackages:
- AnalysisApp
- A class that supports creating a new filter tree (analysis), opening an existing filter tree,
editing the tree and saving changes, and executing an open tree.
- DataFormat
- An enumeration of the data formats supported by the analysis package.
- DiffusionAnalysisFilter
- A filter that performs a diffusion analysis on a set of trajectories.
- IntensityAutoLevelerFilter
- A filter that takes an image array and adjusts the brightness and contrast to equalize intensity
values over the entire range.
- MaximaFinderFilter
- A filter that identifies extrema (maxima or minima) in the input image sequence.
- MetaMorphReaderFilter
- A filter to scan a directory for a set of MetaMorph image series, prompt the user to select a
series from those available, load the series files, then prompt the user to designate
subsequences of the available frames.
This filter relies on the LOCI Bio-Formats libraries to read MetaMorph
files. To obtain these, download "loci_tools.jar" from the
LOCI web site downloads page.
- MotionCompensationFilter
- A filter that compensates for slight motions in the video content, potentially increasing the
size of the frames to contain the shifted images.
- QuicktimeBuilderFilter
- A filter that generates QuickTime movies for each X series in an image array.
- SmootherFilter
- A filter that applies a Gaussian smoothing kernel to every image in an image array.
- TrajectoryFilter
- A filter that generates a set of trajectories from a set of maxima point arrays.
- ZPlaneMergerFilter
- A filter that merges all z planes in an image array, producing a new image array that has 1
plane per time point.
As the author of the source code available by following the links above, I hereby place this source code in the public domain. You can use, modify, and distribute the source code and executable programs based on the source code. However, note the following:
DISCLAIMER OF WARRANTY
This source code is provided "as is" and without any express or implied warranties whatsoever. The user must assume the entire risk of using the source code.