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<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Keck Bioimaging Lab.jpg|240px]]</div>
<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig4 Auer CytometryPartA2018 93-7.jpg|240px]]</div>
'''[[Bioimage informatics]]''' is a multidisciplinary sub-field of [[bioinformatics]] and computational biology that involves the development and use of computational techniques to analyze bioimages, especially cellular and molecular images, on a large scale fashion, with the goal of mining useful knowledge out of complicated and heterogeneous images and related metadata.
'''"[[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 field of bioimage informatics is somewhat related to [[Imaging informatics|medical imaging informatics]], in so much as some of the advances in that field have found their way to the technology of analyzing bioimages. However, "it is very challenging to directly apply existing medical image analysis methods to ... bioimage informatics problems." Some of the challenges bioimages pose to researchers include the difficulty of analyzing at the cellular and molecular scales, the large size of the files, and the amount of time required to manually analyze the files. These challenges require automatic high-throughput analysis techniques, novel algorithms, and advanced systems to deal with the tasks of processing, storing, visualizing, and mining bioimages. ('''[[Bioimage informatics|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 />
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''Recently featured'': [[Biobank]], [[Translational research]], [[Rural health clinic]]
''Recently featured'':
: ▪ [[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:CytoConverter: A web-based tool to convert karyotypes to genomic coordinates|CytoConverter: A web-based tool to convert karyotypes to genomic coordinates]]
: ▪ [[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
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