Difference between revisions of "Journal:Analyzing huge pathology images with open source software"
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'''Keywords''': Digital pathology; Image processing; Virtual slides; Systems biology; ImageJ; NDPI | '''Keywords''': Digital pathology; Image processing; Virtual slides; Systems biology; ImageJ; NDPI | ||
==Background== | |||
Virtual microscopy has become routinely used over the last few years for the transmission of pathology images (the so-called virtual slides), for both telepathology and teaching.<ref name="DiamondVirt09">{{cite book |title=Advanced Techniques in Diagnostic Cellular Pathology |chapter=Virtual Microscopy |author=Diamond, J.; McCleary, D. |editor=Hannon-Fletcher, M.; Maxwell, P. |location=Chichester UK |publisher=John Wiley & Sons, Ltd |year=2009 |isbn=9780470515976}}</ref><ref name="AmeisenStack13">{{cite journal |title=Stack or Trash? Fast quality assessment of virtual slides |journal=Diagnostic Pathology |author=Ameisen, D.; Yunès, J.B.; Deroulers, C.; Perrier, V.; Bouhidel, F.; Battistella, M.; Legrès, L.; Janin, A.; Bertheau, P. |volume=8 |issue=Suppl 1 |pages=S23 |year=2013 |doi=10.1186/1746-1596-8-S1-S23 |pmc=PMC3849546}}</ref> In more and more hospitals, virtual slides are even attached to the patient’s file.<ref name="GarciaCOST11">{{cite journal |title=COST action “EuroTelepath”: digital pathology integration in electronic health record, including primary care centres |journal=Diagnostic Pathology |author=García Rojo, M.; Castro, A.M.; Gonçalves, L. |volume=6 |issue=Suppl 1 |pages=S6 |year=2011 |doi=10.1186/1746-1596-6-S1-S6 |pmid=21489201 |pmc=PMC3073224}}</ref><ref name="AmeisenInt13">{{cite web |title=Intégration des lames virtuelles dans le dossier patient électronique |author=Ameisen, D. |work=PhD thesis |publisher=Univ Paris Diderot-Paris 7 |date=2013}}</ref> They have also a great potential for research, especially in the context of multidisciplinary projects involving e.g. mathematicians and clinicians who do not work at the same location. Quantitative histology is a promising new field, involving computer-based morphometry or statistical analysis of tissues. | |||
A growing number of works report the pertinence of such images for diagnosis and classification of diseases, e.g. tumours [10-14]. Databases of clinical cases [15] will include more and more digitized tissue images. This growing use of virtual microscopy is accompanied by the development of integrated image analysis systems offering both virtual slide scanning and automatic image analysis, which makes integration into the daily practice of pathologists easier. See Ref. [16] for a review of some of these systems. | |||
==References== | ==References== | ||
Revision as of 20:59, 26 September 2015
| Full article title | Analyzing huge pathology images with open source software |
|---|---|
| Journal | Diagnostic Pathology |
| Author(s) | Deroulers, Christophe; Ameisen, David; Badoual, Mathilde; Gerin, Chloé; Granier, Alexandre; Lartaud, Marc |
| Author affiliation(s) | Université Paris Diderot, Université Paris-Sud, Montpellier RIO Imaging, CIRAD |
| Primary contact | Email: deroulers@imnc.in2p3.fr |
| Year published | 2013 |
| Volume and issue | 8 |
| Page(s) | 92 |
| DOI | 10.1186/1746-1596-8-92 |
| ISSN | 1746-1596 |
| Distribution license | Creative Commons Attribution 2.0 Generic |
| Website | http://www.diagnosticpathology.org/content/8/1/92 |
| Download | http://www.diagnosticpathology.org/content/pdf/1746-1596-8-92.pdf (PDF) |
 |
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Abstract
Background
Digital 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.
Results
We 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.
Conclusions
Our 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 slides
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5955513929846272
Keywords: Digital pathology; Image processing; Virtual slides; Systems biology; ImageJ; NDPI
Background
Virtual microscopy has become routinely used over the last few years for the transmission of pathology images (the so-called virtual slides), for both telepathology and teaching.[1][2] In more and more hospitals, virtual slides are even attached to the patient’s file.[3][4] They have also a great potential for research, especially in the context of multidisciplinary projects involving e.g. mathematicians and clinicians who do not work at the same location. Quantitative histology is a promising new field, involving computer-based morphometry or statistical analysis of tissues.
A growing number of works report the pertinence of such images for diagnosis and classification of diseases, e.g. tumours [10-14]. Databases of clinical cases [15] will include more and more digitized tissue images. This growing use of virtual microscopy is accompanied by the development of integrated image analysis systems offering both virtual slide scanning and automatic image analysis, which makes integration into the daily practice of pathologists easier. See Ref. [16] for a review of some of these systems.
References
- ↑ Diamond, J.; McCleary, D. (2009). "Virtual Microscopy". In Hannon-Fletcher, M.; Maxwell, P.. Advanced Techniques in Diagnostic Cellular Pathology. Chichester UK: John Wiley & Sons, Ltd. ISBN 9780470515976.
- ↑ Ameisen, D.; Yunès, J.B.; Deroulers, C.; Perrier, V.; Bouhidel, F.; Battistella, M.; Legrès, L.; Janin, A.; Bertheau, P. (2013). "Stack or Trash? Fast quality assessment of virtual slides". Diagnostic Pathology 8 (Suppl 1): S23. doi:10.1186/1746-1596-8-S1-S23. PMC PMC3849546. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849546.
- ↑ García Rojo, M.; Castro, A.M.; Gonçalves, L. (2011). "COST action “EuroTelepath”: digital pathology integration in electronic health record, including primary care centres". Diagnostic Pathology 6 (Suppl 1): S6. doi:10.1186/1746-1596-6-S1-S6. PMC PMC3073224. PMID 21489201. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3073224.
- ↑ Ameisen, D. (2013). "Intégration des lames virtuelles dans le dossier patient électronique". PhD thesis. Univ Paris Diderot-Paris 7.
Notes
This presentation is faithful to the original, with only a few minor changes to presentation. In most of the article's references DOIs and PubMed IDs were not given; they've been added to make the references more useful. In some cases important information was missing from the references, and that information was added.
