Wavelet-based compression of M-FISH images

Multiplex fluorescence in situ hybridization (M-FISH) is a recently developed technology that enables multi-color chromosome karyotyping for molecular cytogenetic analysis. Each M-FISH image set consists of a number of aligned images of the same chromosome specimen captured at different optical wave...

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Bibliographic Details
Published in:IEEE transactions on biomedical engineering 2005-05, Vol.52 (5), p.890-900
Main Authors: Jianping Hua, Zixiang Xiong, Qiang Wu, Castleman, K.R.
Format: Article
Language:English
Subjects:
Algorithms
Arithmetic
Biological cells
Context model
Context modeling
Continuous wavelet transforms
Data Compression - methods
Design methodology
Fluorescence
hard clustering
Image coding
Image Interpretation, Computer-Assisted - methods
In Situ Hybridization, Fluorescence - methods
lossy-to-lossless compression
M-FISH images
Microscopy, Fluorescence, Multiphoton - methods
molecular cytogenetics
object-based coding
Performance loss
Reproducibility of Results
Sensitivity and Specificity
Signal Processing, Computer-Assisted
Studies
Wavelet domain
Wavelet transforms
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Summary:Multiplex fluorescence in situ hybridization (M-FISH) is a recently developed technology that enables multi-color chromosome karyotyping for molecular cytogenetic analysis. Each M-FISH image set consists of a number of aligned images of the same chromosome specimen captured at different optical wavelength. This paper presents embedded M-FISH image coding (EMIC), where the foreground objects/chromosomes and the background objects/images are coded separately. We first apply critically sampled integer wavelet transforms to both the foreground and the background. We then use object-based bit-plane coding to compress each object and generate separate embedded bitstreams that allow continuous lossy-to-lossless compression of the foreground and the background. For efficient arithmetic coding of bit planes, we propose a method of designing an optimal context model that specifically exploits the statistical characteristics of M-FISH images in the wavelet domain. Our experiments show that EMIC achieves nearly twice as much compression as Lempel-Ziv-Welch coding. EMIC also performs much better than JPEG-LS and JPEG-2000 for lossless coding. The lossy performance of EMIC is significantly better than that of coding each M-FISH image with JPEG-2000.
ISSN:0018-9294
1558-2531
DOI:10.1109/TBME.2005.844269