An automated procedure to properly handle digital images in large scale Tissue Microarray experiments

2005 ◽  
Vol 79 (3) ◽  
pp. 197-208 ◽  
Author(s):  
Rossana Dell’Anna ◽  
Francesca Demichelis ◽  
Mattia Barbareschi ◽  
Andrea Sboner
Keyword(s):  
Tissue Microarray ◽  
Large Scale ◽  
Digital Images ◽  
Microarray Experiments

scholarly journals Tissue Microarray from Cell Block Material (cbTMA)—An Additional Shot for Cytology in the Predictive Pathology Era: The PD-L1 Experience

2022 ◽  
Vol 3 (1) ◽  
pp. 15-23
Author(s):  
Antonino Iaccarino ◽  
Gennaro Acanfora ◽  
Pasquale Pisapia ◽  
Umberto Malapelle ◽  
Claudio Bellevicine ◽  
...  
Keyword(s):  
Tissue Microarray ◽  
Large Scale ◽  
Metastatic Lymph Node ◽  
Predictive Biomarkers ◽  
Predictive Biomarker ◽  
Observer Agreement ◽  
Cell Block ◽  
Multicenter Studies ◽  
Ffpe Samples ◽  
Biomarker Testing

Generally, predictive biomarker tests are clinically validated on histological formalin-fixed, paraffin-embedded (FFPE) samples. In addition to FFPE samples, cytological samples have also emerged as a useful approach to detect predictive biomarkers. However, as of today, despite the promising results reported in the recent literature, their full implementation in routine clinical practice is still lagging owing to a lack of standardized preparatory protocols, challenging assessments of cyto-histological correlation, and variable inter-observer agreement. The aim of this report was to explore the possibility of implementing a large-scale validation of predictive biomarker testing on cytological material. To this aim, we evaluated the technical feasibility of PD-L1 assessment on a cell block (CB)-derived tissue microarray (cbTMA). Consecutive and unselected CBs prepared from metastatic lymph node fine-needle cytology (FNC) samples were retrospectively collected and used for TMA construction. PD-L1 immunohistochemistry (IHC) was carried out on cbTMA sections with the companion diagnostic kit SP263 assay. TMA contained 33 CB-derived cores. A total of 20 sections were hematoxylin and eosin (H&E) stained. Overall, 29 (88%) samples were visible at least in one H&E-stained slide. Four cases out of five sections stained with the SP263 assay (4/29, 13.8%) showed PD-L1 positivity in neoplastic and/or immune cells; remarkably, no unspecific background was observed. Although our study was based on a limited and non-selected series, our findings do provide proof of concept for the use of cbTMA in predictive biomarker testing on cytological material in large-scale post-clinical trial validation studies, multicenter studies, and quality control programs.

Flow Visualization and Leakage Measurements of Stepped Labyrinth Seals: Part 1—Annular Groove

1997 ◽  
Vol 119 (4) ◽  
pp. 839-843 ◽  
Author(s):  
D. L. Rhode ◽  
J. W. Johnson ◽  
D. H. Broussard
Keyword(s):  
Flow Visualization ◽  
Large Scale ◽  
Digital Images ◽  
Test Facility ◽  
Labyrinth Seals ◽  
Water Leakage ◽  
Tracer Particles ◽  
Leakage Resistance ◽  
Visualization Experiments ◽  
Resistance Improvement

An improved understanding of a new category of stepped labyrinth seals, which feature a new “annular groove,” was obtained. A water leakage and flow visualization test facility of very large scale (relative to a typical seal) was utilized. Flow visualization experiments using a new method and digital facilities for capturing and editing digital images from an 8 mm video were conducted. The presence of an annular groove machined into the stator land increases the leakage resistance by up to 26 percent for the cases considered here. Tracer particles show the degree of throughflow path penetration into the annular groove (i.e., serpentining), which gives the largest and the smallest leakage resistance improvement over that of the corresponding conventional stepped seal.

scholarly journals PENERAPAN DIGITAL WATERMARK SEBAGAI VALIDASI KEABSAHAN GAMBAR DIGITAL DENGAN SKEMA BLIND WATERMARK

2017 ◽  
Vol 3 (2) ◽  
Author(s):  
Adi Suheryadi
Keyword(s):  
Digital Watermarking ◽  
Digital Image ◽  
Large Scale ◽  
Digital Images ◽  
Technological Development ◽  
Mean Value ◽  
Secret Key ◽  
Legal Cases ◽  
News Reporting ◽  
Digital Era

Digital watermarking is an important field of technological development that has now grown in the digital era. Digital era encourage the spread digital images on internet by the websites with a large scale. On the other hand, digital images are objects that are very easy to change or manipulate, and even copied irresponsibly. Meanwhile it is very difficult to prove the image has been changed by existing equipment at this time, and it is difficult to prove its ownership. This is an important issue, when the image is one of the evidences for legal cases, news reporting and medical filing, where the image must be ensured that the digital image is not subject to change or manipulation. In this paper, we present the application of digital watermarking to authentication and ownership validation of digital image so the image can be ascertained its validity. This research applies blind watermark scheme by using secret key that inserted at least-significant bits (LSB) of host image therefore the watermark is invisible watermark. The result of watermarked image has a small decrease in quality with the mean value of PSNR and MSE about 34.08 and 14.62.

scholarly journals A Seven-Marker Signature and Clinical Outcome in Malignant Melanoma: A Large-Scale Tissue-Microarray Study with Two Independent Patient Cohorts

PLoS ONE ◽  
2012 ◽  
Vol 7 (6) ◽  
pp. e38222 ◽  
Author(s):  
Stefanie Meyer ◽  
Thomas J. Fuchs ◽  
Anja K. Bosserhoff ◽  
Ferdinand Hofstädter ◽  
Armin Pauer ◽  
...  
Keyword(s):  
Malignant Melanoma ◽  
Clinical Outcome ◽  
Tissue Microarray ◽  
Large Scale ◽  
Microarray Study

Information Technology of Color Imaging Assessment of Saccharomyces cerevisiae UCM Y-517 Yeast Volutin Granules

2020 ◽  
Vol 82 (5) ◽  
pp. 30-35
Author(s):  
O.M. Gromozova ◽  
◽  
T.L. Kachur ◽  
V.V. Vishnevsky ◽  
O.S. Sychev ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Information Technology ◽  
Large Scale ◽  
Digital Images ◽  
Yeast Cells ◽  
Qualitative Assessment ◽  
Color Imaging ◽  
Daily Monitoring ◽  
Web Resource ◽  
Software Algorithms

The research is devoted to the development of color imaging information technology, which is relevant for evaluating the results of cytochemical research in both biology and medicine. The aim of this work was to study the validity of software algorithms and integrated information technology for the qualitative and quantitative analysis of metachromasia reaction of volutin granules of Saccharomyces cerevisiae UCM Y-517 yeast. Methods. The object of this study was Saccharomyces cerevisiae UCM Y-517 yeast from the Ukrainian collection of microorganisms. The yeast was cultivated for 24 hours at 28oC. The metachromatic reaction of volutin granules was detected microscopically by the preparation of yeast cells stained with methylene blue. Digital images of cells were transferred to a specialized web resource for computer processing. Results. The algorithm of computer analysis of images included 3 steps: (1) recognition of single volutin granules, (2) assessment of the magnitude of metachromasia for each granule, and (3) integral estimation of the magnitude of metachromasia for the whole image. Information technology was developed and tested to support the daily monitoring of the metachromasia phenomenon, including obtaining the digital images, their transfer to a remote server, and automatic processing. Information technology is integrated into the web portal of the large-scale biophysical experiment “Heliomed”. Conclusions. The proposed method of computer image processing gave a quantitative and qualitative assessment in the automatic mode of metachromatic staining of volutin granules and confirmed the previously proposed classification of this phenomenon on the basis of visual examination.

scholarly journals Finding Groups in Gene Expression Data

2005 ◽  
Vol 2005 (2) ◽  
pp. 215-225 ◽  
Author(s):  
David J. Hand ◽  
Nicholas A. Heard
Keyword(s):  
Cluster Analysis ◽  
Regulatory Networks ◽  
Large Scale ◽  
Disease Diagnosis ◽  
Expression Data ◽  
Data Set ◽  
Microarray Experiments ◽  
Data Analyst ◽  
Bump Hunting ◽  
Function Discovery

The vast potential of the genomic insight offered by microarray technologies has led to their widespread use since they were introduced a decade ago. Application areas include gene function discovery, disease diagnosis, and inferring regulatory networks. Microarray experiments enable large-scale, high-throughput investigations of gene activity and have thus provided the data analyst with a distinctive, high-dimensional field of study. Many questions in this field relate to finding subgroups of data profiles which are very similar. A popular type of exploratory tool for finding subgroups is cluster analysis, and many different flavors of algorithms have been used and indeed tailored for microarray data. Cluster analysis, however, implies a partitioning of the entire data set, and this does not always match the objective. Sometimes pattern discovery or bump hunting tools are more appropriate. This paper reviews these various tools for finding interesting subgroups.

Fast Large Scale Oligonucleotide Selection Using the Longest Common Factor Approach

2003 ◽  
Vol 01 (02) ◽  
pp. 343-361 ◽  
Author(s):  
Sven Rahmann
Keyword(s):  
Large Scale ◽  
Selection Process ◽  
Common Factor ◽  
Suffix Array ◽  
Fast Method ◽  
Microarray Experiments ◽  
Additional Information ◽  
Human Genes ◽  
Longest Common Substring ◽  
Specificity Measure

We present a fast method that selects oligonucleotide probes (such as DNA 25-mers) for microarray experiments on a truly large scale. For example, reliable oligos for human genes can be found within four days, a speedup of one to two orders of magnitude compared to previous approaches. This speed is attained by using the longest common substring as a specificity measure for candidate oligos. We present a space- and time-efficient algorithm, based on a suffix array with additional information, to compute matching statistics (lengths of longest matches) between all candidate oligos and all remaining sequences. With the matching statistics available, we show how to incorporate constraints such as oligo length, melting temperature, and self-complementarity into the selection process at a postprocessing stage. As a result, we can now design custom oligos for any sequenced genome, just as the technology for on-site chip synthesis is becoming increasingly mature.

scholarly journals Statistical process control for large scale microarray experiments

2002 ◽  
Vol 18 (Suppl 1) ◽  
pp. S155-S163 ◽  
Author(s):  
F. Model ◽  
T. Konig ◽  
C. Piepenbrock ◽  
P. Adorjan
Keyword(s):  
Process Control ◽  
Statistical Process Control ◽  
Large Scale ◽  
Statistical Process ◽  
Microarray Experiments
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