Open source tools for management and archiving of digital microscopy data to allow integration with patient pathology and treatment information

Khushi, Matloob; Edwards, Georgina; Marcos, Diego Alonso de; Carpenter, Jane; Graham, J. Dinny

doi:10.1186/1746-1596-8-22

Cited by 15 publications

(9 citation statements)

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“…The Australian Breast Cancer Tissue Bank (ABCTB) Jane E. Carpenter, 1 Deborah Marsh, 2 Mythily Mariasegaram 3 and Christine L. Clarke 4 The ABCTB was established in 2006 as an open access, not for profit resource dedicated to providing biospecimens and/or data to both national and international research projects in the field of breast cancer. Donors are consented according to standard ethical principles for use of their material for unspecified future research.…”

Section: Bioresource Papermentioning

confidence: 99%

“…Both tissue and blood samples are collected and stored and a central processing laboratory is able to perform DNA and RNA extractions, sectioning of tissue, creation of Tissue Micro Arrays (TMAs) and digital imaging of stained sections of tumour. The latter are made available for viewing on the ABCTB website [4] so that researchers can review and select individual cases. Data is collected via both electronic and manual methods.…”

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The Australian Breast Cancer Tissue Bank (ABCTB)

Carpenter

Marsh

Mariasegaram

et al. 2014

Open Journal of Bioresources

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The ABCTB was established in 2006 as an open access, not for profit resource dedicated to providing bio-specimens and/or data to both national and international research projects in the field of breast cancer. Donors are consented according to standard ethical principles for use of their material for unspecified future research. ABCTB collects fully annotated clinical samples and associated clinical and longitudinal data from donors. Material and data is supplied to research projects.

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Section: Bioresource Papermentioning

confidence: 99%

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confidence: 99%

The Australian Breast Cancer Tissue Bank (ABCTB)

Carpenter

Marsh

Mariasegaram

et al. 2014

Open Journal of Bioresources

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“…OpenSlide [24] does not currently support the NDPI format. NDPI-Splitter [26] needs to be run on Windows and depends on a proprietary library.…”

Section: Introductionmentioning

confidence: 99%

Analyzing huge pathology images with open source software

et al. 2013

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BackgroundDigital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer’s memory. Moreover, there is no standard format. Therefore, most common open source tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow.ResultsWe have developed several cross-platform open source software tools to overcome these limitations. The NDPITools provide a way to transform microscopy images initially in the loosely supported NDPI format into one or several standard TIFF files, and to create mosaics (division of huge images into small ones, with or without overlap) in various TIFF and JPEG formats. They can be driven through ImageJ plugins. The LargeTIFFTools achieve similar functionality for huge TIFF images which do not fit into RAM. We test the performance of these tools on several digital slides and compare them, when applicable, to standard software. A statistical study of the cells in a tissue sample from an oligodendroglioma was performed on an average laptop computer to demonstrate the efficiency of the tools.ConclusionsOur open source software enables dealing with huge images with standard software on average computers. They are cross-platform, independent of proprietary libraries and very modular, allowing them to be used in other open source projects. They have excellent performance in terms of execution speed and RAM requirements. They open promising perspectives both to the clinician who wants to study a single slide and to the research team or data centre who do image analysis of many slides on a computer cluster.Virtual slidesThe virtual slide(s) for this article can be found here:http://www.diagnosticpathology.diagnomx.eu/vs/5955513929846272

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“…The latter are made available for viewing on the ABCTB website [4] so that researchers can review and select individual cases. Data is collected via both electronic and manual methods.…”

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confidence: 99%

Australian Breast Cancer Tissue Bank (ABCTB)

2011

Biopreservation and Biobanking

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Open source tools for management and archiving of digital microscopy data to allow integration with patient pathology and treatment information

Cited by 15 publications

References 13 publications

The Australian Breast Cancer Tissue Bank (ABCTB)

The Australian Breast Cancer Tissue Bank (ABCTB)

Analyzing huge pathology images with open source software

Australian Breast Cancer Tissue Bank (ABCTB)

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