Splitting bits for lossless compression of microarray images

Lossless gray scale image compression is necessary for many purposes, such as medical imaging, image databases and so on. Lossy images are important as well, because of the high compression ratio. The authors propose a lossless image compression scheme using a lossy image generated with the JPEG-DCT scheme. The concept is, send a JPEG-compressed lossy image primarily, then send residual information and reconstruct the original image using both the lossy image and residual information. 3D adaptive prediction and adaptive arithmetic coding are used, which fully use the statistical parameters of the distribution of the symbol source. The optimal number of neighbor pixels and lossy pixels used for prediction is discussed. The compression ratio is better than previous work and quite close to the original lossless algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

In a color-mapped (pseudo-color) image, pixel values repre- sent indices that point to color values in a look-up table. Well-known linear predictive schemes, such as JPEG and CALIC, perform poorly when used with pseudo-color images, while universal compressors, such as Gzip, Pkzip and Compress, yield better compression gain. Recently, Burrows and Wheeler introduced the Block Sorting Lossless Data Com- pression Algorithm (BWA). The BWA algorithm received considerable attention. It achieves compression rates as good as context-based meth- ods, such as PPM, but at execution speeds closer to Ziv-Lempel tech- niques. The BWA algorithm is mainly composed of a block-sorting trans- formation which is known as Burrows-Wheeler Transformation (BWT), followed by Move-To-Front (MTF) coding. We introduce a new block transformation, Linear Order Transformation (LOT). We delineate its re- lationship to Burrows-Wheeler Transformation and show that LOT is faster than BWT transformation. We then show that when MTF coder is employed after the LOT, the compression gain obtained is better than the well-known compression techniques, such as GIF, JPEG, CALIC, Gzip, LZW (Unix Compress) and the BWA for pseudo-color images.

A spot-adaptive compound clustering-enhancement-segmentation (CES) scheme was developed for the quantification of gene expression levels in microarray images. The CES-scheme employed 1/griding, for locating spot-regions, 2/Fuzzy C-means clustering, for segmenting spots from background, 3/ background noise estimation and spot's center localization, 4/emphasizing of spot's outline by the CLAHE image enhancement technique, 5/segmentation by the SRG algorithm, using information from step 3, and 6/microarray spot intensity extraction. Extracted intensities by the CES-Scheme were compared against those obtained by the MAGIC TOOL's SRG. Kullback-Liebler metric's values for the CES-Scheme were on average double than MAGIC TOOL's, with differences ranging from 1.45bits to 2.77bits in 7 cDNA images. Coefficient-of-Variation results showed significantly higher reproducibility (p<0.001) for the CES-Scheme in quantifying gene expression levels. Processing times for 1024×1024 16-bit microarray images containing 6400 spots were 300 and 487 seconds for the CES-Scheme and MAGIC TOOL respectively.

A simple lossy-to-lossless bit-plane coding of still images is presented to integrate several functionality extensions including selective tile partitioning, progressive transmission, ROI transmission, accuracy scalability, and others. The mean squared error between the original image and a decoded image at any progression level is known prior to encoding/decoding. The proposed bit-plane codec is competitive with JPEG-LS and JPEG 2000 in the lossless compression of 8-bit grayscale and 24-bit color images. The codec outperforms the existing standards in 8-bit color-quantized image compression.

Microarray image compression: SLOCO and the effect of information loss

Current gene-expression microarrays carry enormous amounts of information. Compression is necessary for efficient distribution and storage. This paper examines JPEG2000 compression of cDNA microarray images and addresses the accuracy of classification and feature selection based on decompressed images. Among other options, we choose JPEG2000 because it is the latest international standard for image compression and offers lossy-to-lossless compression while achieving high lossless compression ratios on microarray images. The performance of JPEG2000 has been tested on three real data sets at different compression ratios, ranging from lossless to 45:1. The effects of JPEG2000 compression/decompression on differential expression detection and phenotype classification have been examined. There is less than a 4% change in differential detection at compression rates as high as 20:1, with detection accuracy suffering less than 2% for moderate to high intensity genes, and there is no significant effect on classification at rates as high as 35:1. The supplementary material is available at http://gsp.tamu.edu/web2/Compression.

Problem statement: Existing lossless image compression schemes attempt to do prediction in an image data using their Local Binary Pattern ( LBP) and their spatial neighborhood based techniques. In the previous techniques such as Vec tor Quantization (VQ) and Gradient Adjusted Prediction (GAP) the texture and non-texture region s are not classified separately. Texture and Non- texture images prophecy has been a key factor in ef ficient lossless image compression. Hence, there is a need to develop a more efficient image prediction scheme to exploit these texture components. Approach: In this research, an efficient visual quality tech nique for image compression is proposed. The image is classified into texture and non-textur e regions by using an Artificial Neural Network (ANN) Classifier. The texture region is encoded wit h the Similar Block Matching (SBM) encoder and the non-texture region is encoded with SPIHT encoding. Results: The proposed texture prediction based compression is compared with the existing compression techniques such as H.264 and JPEG. From the result it reveals that the Peak Signal to Noise Ratio (PSNR) values of all the test images is higher in the proposed technique as compared to JPE G technique. Similarly PSNR values are low in H.264 for all the images except Boat image when compared to the proposed technique. This result concludes that the increase in PSNR indicates that the output image has less noise as compared to existing techniques. Conclusion: The compression of the proposed algorithm is superi or to JPEG and H.264. Our new method of compression algorithm can be used to improve the performance of Compression ratio and Peak Signal to Noise Ratio (P SNR). In future this study can be extended to real time applications for video compression in medical images.

With widespread use of screening digital mammography, efficient storage of the vast amounts of data has become a challenge. While lossless image compression causes no risk to the interpretation of the data, it does not allow for high compression rates. Lossy compression and the associated higher compression ratios are therefore more desirable. The U.S. Food and Drug Administration (FDA) currently interprets the Mammography Quality Standards Act as prohibiting lossy compression of digital mammograms for primary image interpretation, image retention, or transfer to the patient or her designated recipient. Previous work has used reader studies to determine proper usage criteria for evaluating lossy image compression in mammography, and utilized different measures and metrics to characterize medical image quality. The drawback of such studies is that they rely on a threshold on compression ratio as the fundamental criterion for preserving the quality of images. However, compression ratio is not a useful indicator of image quality. On the other hand, many objective image quality metrics (IQMs) have shown excellent performance for natural image content for consumer electronic applications. In this paper, we create a new synthetic mammogram database with several unique features. We compare and characterize the impact of image compression on several clinically relevant image attributes such as perceived contrast and mass appearance for different kinds of masses. We plan to use this database to develop a new objective IQM for measuring the quality of compressed mammographic images to help determine the allowed maximum compression for different kinds of breasts and masses in terms of visual and diagnostic quality.

BackgroundMicroarray image analysis processes scanned digital images of hybridized arrays to produce the input spot-level data for downstream analysis, so it can have a potentially large impact on those and subsequent analysis. Signal saturation is an optical effect that occurs when some pixel values for highly expressed genes or peptides exceed the upper detection threshold of the scanner software (216 - 1 = 65, 535 for 16-bit images). In practice, spots with a sizable number of saturated pixels are often flagged and discarded. Alternatively, the saturated values are used without adjustments for estimating spot intensities. The resulting expression data tend to be biased downwards and can distort high-level analysis that relies on these data. Hence, it is crucial to effectively correct for signal saturation.ResultsWe developed a flexible mixture model-based segmentation and spot intensity estimation procedure that accounts for saturated pixels by incorporating a censored component in the mixture model. As demonstrated with biological data and simulation, our method extends the dynamic range of expression data beyond the saturation threshold and is effective in correcting saturation-induced bias when the lost information is not tremendous. We further illustrate the impact of image processing on downstream classification, showing that the proposed method can increase diagnostic accuracy using data from a lymphoma cancer diagnosis study.ConclusionsThe presented method adjusts for signal saturation at the segmentation stage that identifies a pixel as part of the foreground, background or other. The cluster membership of a pixel can be altered versus treating saturated values as truly observed. Thus, the resulting spot intensity estimates may be more accurate than those obtained from existing methods that correct for saturation based on already segmented data. As a model-based segmentation method, our procedure is able to identify inner holes, fuzzy edges and blank spots that are common in microarray images. The approach is independent of microarray platform and applicable to both single- and dual-channel microarrays.

Image processing is the field of signal processing where both the input and output signals are images. Images can be thought of as two-dimensional signals via a matrix representation. Image processing a is very important subject, and finds itself in such fields as photography, satellite imaging, medical imaging, and image compression, to name but a few. In the past, image processing was largely done using analog devices (Cheng et al., 2006). However, as computers became more powerful, processing shifted toward the digital domain. Like one-dimensional digital signal processing, digital image processing overcomes traditional analog problems such as noise, distortion during processing, inflexibility of system to change, and difficulty of implementation. Image retrieval, popularly referred to as content-based image retrieval is an emerging technology that allows a user to retrieve relevant images in an effective and efficient manner. Digital imaging has extensive applications in our daily lives and it is being used for several applications. Examples of imaging applications are in museums for archiving important images and manuscripts from art gallery and museum management. Many useful applications of imaging are found in security for tracking an intruder, crime prevention, law enforcement and object recognition in digital forensic. In particular, image retrieval is potentially useful in discovering brain activation patterns, in classifications and in diagnoses by comparing observed patterns with those of known diseases, leading to clinical applications. In biomedicine, content-based image retrieval is critically important in patient digital libraries, clinical diagnosis, clinical trials, searching for 2-D electrophoresis gels, and pathological slides. Most existing content-based image retrieval systems (Flickner et al., 1995; Gupta and Jain, 1997; Ma and Manjunath, 1997; Rubner, 1999 and Wang et al., 1998) are designed for general purpose picture libraries such as photos and graph. The storage, manipulation and analysis of the contents of digital images are essential requirements for the next generation of healthcare information infrastructure. The aim of this infrastructure is to bring timely health information to support communication among healthcare decision makers and communities at large. Among several healthcare services that can be provided with the aid of the emerging grid technology for ubiquitous access, image classification and diagnosis services are important. The ubiquitous access and

Automation for leather grading system is an emerging technology in the leather industries. The leather surface images are rich in texture and results in large file sizes. Hence it needs high storage capacity and the computation time required to process these images is also huge. Image compression has become crucial in relation to processing, storage as well as for transmission. Lossy and lossless are the two compression techniques used widely and lossless compression is preferred for archival purposes. The aim is to present a very efficient image compression technique to reduce the computational complexity of the leather grading system and to store the leather images effectively. Our proposed methodology is to compress an image using second generation wavelets by introducing Lifting Scheme which provides the frame for building the Multiwavelet. The image is compressed by Set Partition in Hierarchical Tree (SPIHT) coding. According to the experimental results, the computational time for leather grading system is considerably reduced by compressing the image. The image is processed 42 % faster than the uncompressed image.

DNA microarray images, which are the final results of a microarray experiment, are usually massive in size. We have designed and implemented an algorithm for lossy compression of microarray images. First, spots are automatically extracted into spot sub-images. Then, within each subimage, a circle is matched to each spot. This is done via spatial optimization techniques. After that, our circle to square transform, C2S, is applied to the sub-image and a square image representing its spot part is achieved. Information regarding the coordinates of the C2S transform is also included in the final compressed file. The background parts which contain no biological information are neglected. The square shaped images are then put together and coded by means of DCT transform, quantization, and entropy coding.

Today is the digital era and the human being is surrounded by digital gadgets. Now a days, photography is a part of human being's daily life and digital images are widely used in computer applications. As the megapixels of the digital cameras are increasing, more storage memory is required and at the same time more bandwidth is needed for transmission of digital images. This results in need of image compression. This paper explains the use of Legendre polynomials for lossy and lossless image compression. Different approximations for image transformation have been evaluated as 1-D Legendre polynomials, 1-D adaptive Legendre polynomials, 2-D Legendre polynomials and 2-D adaptive Legendre polynomials. Moreover, the performance of different image scanning methods have been tested. Results have been compared in terms of peak signal-to-noise ratio (PSNR), nominal compression rate (NCR), mean structural similarity (MSSIM) and compression ratio in order to minimize the difference between the approximated polynomial output and the original pixel gray level.

In this paper, we propose a new low bit rate scheme that combines the Discrete Wavelet transform (IWT) and Vector Quantization (VQ) for image compression with high Compression Ratio (CR) in order to achieve acceptable quality of output images, Image compression using the combination of DWT willy VQ has been considered in many recent works; here in our paper the DWT was performed on several gray scale standard images, each of (256X256) byte. We used 4 images as the training images of the train VO using LBG algorithm and got the final optimal codebook. Then we used another two images to compare our output image with JPEG 2000 standard winch based on Wavelet and Scalar quantization. Our proposed system used a VO codebook with Variable cod hook size and dimensions were used to compress wavelet Transform) coefficients resulting using Danny wavelet types. Our pro system is slowed so that the best Wavelet types that you can use for compression is COIF 2. Our proposed system gave better PSNR than G2000 standard at high (CR), above than (5L), and this achieved a VQ codebook size (1024 -512) with dimension equal to 256. In the paper a typical system for the application of image compression system and new scientific results are present.

Apart from the existing technology on image compression represented by series of JPEG, MPEG and H.26x standards, new technology such as Wavelet Neural Networks (WNN) and genetic algorithms are being developed to explore the future of image coding. Successful applications of WNN in the case of function approximation become well established. This paper presents a direct solution method based on Multi Library WNN for color image compression and coding which consists to transform an RGB image into Luminance-Chrominance space and then segment the luminance in a set of m blocks n by n pixels. These blocks should be transferred row by row (1D input vector) to the input of our wavelet network. Every input vector will be considered as unknown functional mapping and then it will be approximated by the network.