Wndchrm - an open source utility for biological image analysis
Biological imaging is an emerging field, covering a wide range of applications in biological and clinical research. However, while machinery for automated experimenting and data acquisition have been developing rapidly in the past years, automated image analysis often introduces a bottleneck in high content screening.
Methods: Wndchrm is an open source utility for biological image analysis.
The software works by first extracting image content descriptors from the raw image, image transforms, and compound image transforms. Then, the most informative features are selected, and the images are analyzed.
Results: Wndchrm has been tested using several publicly available biological datasets, and provided results which are favorably comparable to the performance of task-specific algorithms developed for these datasets.
The simple user interface allows researchers who are not knowledgeable in computer vision methods and have no background in computer programming to apply image analysis to their data.
Conclusions: We suggest that wndchrm can be effectively used for a wide range of biological image analysis tasks. Using wndchrm can allow scientists to perform automated biological image analysis while avoiding the costly challenge of implementing computer vision and pattern recognition algorithms.
Author: Lior Shamir, Nikita Orlov, D. Mark Eckley, Tomasz Macura, Josiah Johnston and Ilya Goldberg
Credits/Source: Source Code for Biology and Medicine 2008, 3:13
Published on: 2008-07-08
Copyright by the authors listed above - made available via BioMedCentral (Open Access). Please
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