Difference between revisions of "Template:Article of the week"

From LIMSWiki
Jump to navigationJump to search
(Updated article of the week text.)
(Updated article of the week text)
(113 intermediate revisions by the same user not shown)
Line 1: Line 1:
<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig1 Mayernik BigDataSoc2017 4-2.gif|240px]]</div>
<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig4 Auer CytometryPartA2018 93-7.jpg|240px]]</div>
'''"[[Journal:Open data: Accountability and transparency|Open data: Accountability and transparency]]"'''
'''"[[Journal:ChromaWizard: An open-source image analysis software for multicolor fluorescence in situ hybridization analysis|ChromaWizard: An open-source image analysis software for multicolor fluorescence in situ hybridization analysis]]"'''


The movements by national governments, funding agencies, universities, and research communities toward “open data” face many difficult challenges. In high-level visions of open data, researchers’ data and metadata practices are expected to be robust and structured. The integration of the internet into scientific institutions amplifies these expectations. When examined critically, however, the data and metadata practices of scholarly researchers often appear incomplete or deficient. The concepts of “accountability” and “transparency” provide insight in understanding these perceived gaps. Researchers’ primary accountabilities are related to meeting the expectations of research competency, not to external standards of data deposition or metadata creation. Likewise, making data open in a transparent way can involve a significant investment of time and resources with no obvious benefits. This paper uses differing notions of accountability and transparency to conceptualize “open data” as the result of ongoing achievements, not one-time acts. ('''[[Journal:Open data: Accountability and transparency|Full article...]]''')<br />
Multicolor image analysis finds its applications in a broad range of biological studies. Specifically, multiplex [[wikipedia:Fluorescence in situ hybridization|fluorescence ''in situ'' hybridization]] (M‐FISH) for chromosome painting facilitates the analysis of individual chromosomes in complex metaphase spreads and is widely used to detect both numerical and structural aberrations. While this is well established for human and mouse [[wikipedia:Karyotype|karyotypes]], for which species sophisticated software and analysis tools are available, other organisms and species are less well served. Commercially available software is proprietary and not easily adaptable to other karyotypes. Therefore, a publicly available open-source software that combines flexibility and customizable functionalities is needed. Here we present such a tool, called “ChromaWizard,” which is based on popular scientific image analysis libraries (OpenCV, scikit‐image, and NumPy). We demonstrate its functionality on the example of primary Chinese hamster (''Cricetulus griseus'') fibroblasts metaphase spreads and on Chinese hamster ovary cell lines, known for their large number of chromosomal rearrangements. ('''[[Journal:ChromaWizard: An open-source image analysis software for multicolor fluorescence in situ hybridization analysis|Full article...]]''')<br />
<br />
<br />
''Recently featured'':  
''Recently featured'':
: ▪ [[Journal:Recommended versus certified repositories: Mind the gap|Recommended versus certified repositories: Mind the gap]]
: ▪ [[Journal:Haves and have nots must find a better way: The case for open scientific hardware|Haves and have nots must find a better way: The case for open scientific hardware]]
: ▪ [[Journal:Usability evaluation of laboratory information systems|Usability evaluation of laboratory information systems]]
: ▪ [[Journal:CytoConverter: A web-based tool to convert karyotypes to genomic coordinates|CytoConverter: A web-based tool to convert karyotypes to genomic coordinates]]
: ▪ [[Journal:Data management: New tools, new organization, and new skills in a French research institute|Data management: New tools, new organization, and new skills in a French research institute]]
: ▪ [[Journal:Implementing a novel quality improvement-based approach to data quality monitoring and enhancement in a multipurpose clinical registry|Implementing a novel quality improvement-based approach to data quality monitoring and enhancement in a multipurpose clinical registry]]

Revision as of 22:58, 24 February 2020

Fig4 Auer CytometryPartA2018 93-7.jpg

"ChromaWizard: An open-source image analysis software for multicolor fluorescence in situ hybridization analysis"

Multicolor image analysis finds its applications in a broad range of biological studies. Specifically, multiplex fluorescence in situ hybridization (M‐FISH) for chromosome painting facilitates the analysis of individual chromosomes in complex metaphase spreads and is widely used to detect both numerical and structural aberrations. While this is well established for human and mouse karyotypes, for which species sophisticated software and analysis tools are available, other organisms and species are less well served. Commercially available software is proprietary and not easily adaptable to other karyotypes. Therefore, a publicly available open-source software that combines flexibility and customizable functionalities is needed. Here we present such a tool, called “ChromaWizard,” which is based on popular scientific image analysis libraries (OpenCV, scikit‐image, and NumPy). We demonstrate its functionality on the example of primary Chinese hamster (Cricetulus griseus) fibroblasts metaphase spreads and on Chinese hamster ovary cell lines, known for their large number of chromosomal rearrangements. (Full article...)

Recently featured:

Haves and have nots must find a better way: The case for open scientific hardware
CytoConverter: A web-based tool to convert karyotypes to genomic coordinates
Implementing a novel quality improvement-based approach to data quality monitoring and enhancement in a multipurpose clinical registry