Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 Bringing Open Data to Whole Slide Imaging.

Literature DB >> 31579322

Bringing Open Data to Whole Slide Imaging.

Sébastien Besson¹, Roger Leigh¹, Melissa Linkert², Chris Allan², Jean-Marie Burel¹, Mark Carroll¹, David Gault¹, Riad Gozim¹, Simon Li¹, Dominik Lindner¹, Josh Moore¹, Will Moore¹, Petr Walczysko¹, Frances Wong¹, Jason R Swedlow^1,2.

Abstract

Faced with the need to support a growing number of whole slide imaging (WSI) file formats, our team has extended a long-standing community file format (OME-TIFF) for use in digital pathology. The format makes use of the core TIFF specification to store multi-resolution (or "pyramidal") representations of a single slide in a flexible, performant manner. Here we describe the structure of this format, its performance characteristics, as well as an open-source library support for reading and writing pyramidal OME-TIFFs.

Entities: Chemical

Keywords: OME-TIFF; open data; open file format; whole slide imaging

Year: 2019 PMID： 31579322 PMCID： PMC6774793 DOI： 10.1007/978-3-030-23937-4_1

Source DB: PubMed Journal: Digit Pathol (2019)

22 in total

1. Perinodular and Intranodular Radiomic Features on Lung CT Images Distinguish Adenocarcinomas from Granulomas.

Authors: Niha Beig; Mohammadhadi Khorrami; Mehdi Alilou; Prateek Prasanna; Nathaniel Braman; Mahdi Orooji; Sagar Rakshit; Kaustav Bera; Prabhakar Rajiah; Jennifer Ginsberg; Christopher Donatelli; Rajat Thawani; Michael Yang; Frank Jacono; Pallavi Tiwari; Vamsidhar Velcheti; Robert Gilkeson; Philip Linden; Anant Madabhushi
Journal: Radiology Date: 2018-12-18 Impact factor: 11.105

2. Proteomics. Tissue-based map of the human proteome.

Authors: Mathias Uhlén; Linn Fagerberg; Björn M Hallström; Cecilia Lindskog; Per Oksvold; Adil Mardinoglu; Åsa Sivertsson; Caroline Kampf; Evelina Sjöstedt; Anna Asplund; IngMarie Olsson; Karolina Edlund; Emma Lundberg; Sanjay Navani; Cristina Al-Khalili Szigyarto; Jacob Odeberg; Dijana Djureinovic; Jenny Ottosson Takanen; Sophia Hober; Tove Alm; Per-Henrik Edqvist; Holger Berling; Hanna Tegel; Jan Mulder; Johan Rockberg; Peter Nilsson; Jochen M Schwenk; Marica Hamsten; Kalle von Feilitzen; Mattias Forsberg; Lukas Persson; Fredric Johansson; Martin Zwahlen; Gunnar von Heijne; Jens Nielsen; Fredrik Pontén
Journal: Science Date: 2015-01-23 Impact factor: 47.728

3. Diagnostic Assessment of Deep Learning Algorithms for Detection of Lymph Node Metastases in Women With Breast Cancer.

Authors: Babak Ehteshami Bejnordi; Mitko Veta; Paul Johannes van Diest; Bram van Ginneken; Nico Karssemeijer; Geert Litjens; Jeroen A W M van der Laak; Meyke Hermsen; Quirine F Manson; Maschenka Balkenhol; Oscar Geessink; Nikolaos Stathonikos; Marcory Crf van Dijk; Peter Bult; Francisco Beca; Andrew H Beck; Dayong Wang; Aditya Khosla; Rishab Gargeya; Humayun Irshad; Aoxiao Zhong; Qi Dou; Quanzheng Li; Hao Chen; Huang-Jing Lin; Pheng-Ann Heng; Christian Haß; Elia Bruni; Quincy Wong; Ugur Halici; Mustafa Ümit Öner; Rengul Cetin-Atalay; Matt Berseth; Vitali Khvatkov; Alexei Vylegzhanin; Oren Kraus; Muhammad Shaban; Nasir Rajpoot; Ruqayya Awan; Korsuk Sirinukunwattana; Talha Qaiser; Yee-Wah Tsang; David Tellez; Jonas Annuscheit; Peter Hufnagl; Mira Valkonen; Kimmo Kartasalo; Leena Latonen; Pekka Ruusuvuori; Kaisa Liimatainen; Shadi Albarqouni; Bharti Mungal; Ami George; Stefanie Demirci; Nassir Navab; Seiryo Watanabe; Shigeto Seno; Yoichi Takenaka; Hideo Matsuda; Hady Ahmady Phoulady; Vassili Kovalev; Alexander Kalinovsky; Vitali Liauchuk; Gloria Bueno; M Milagro Fernandez-Carrobles; Ismael Serrano; Oscar Deniz; Daniel Racoceanu; Rui Venâncio
Journal: JAMA Date: 2017-12-12 Impact factor: 56.272

4. The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging.

Authors: Ilya G Goldberg; Chris Allan; Jean-Marie Burel; Doug Creager; Andrea Falconi; Harry Hochheiser; Josiah Johnston; Jeff Mellen; Peter K Sorger; Jason R Swedlow
Journal: Genome Biol Date: 2005-05-03 Impact factor: 13.583

5. Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes.

Authors: Jia-Ren Lin; Benjamin Izar; Shu Wang; Clarence Yapp; Shaolin Mei; Parin M Shah; Sandro Santagata; Peter K Sorger
Journal: Elife Date: 2018-07-11 Impact factor: 8.140

6. Standardization in digital pathology: Supplement 145 of the DICOM standards.

Authors: Rajendra Singh; Lauren Chubb; Liron Pantanowitz; Anil Parwani
Journal: J Pathol Inform Date: 2011-05-11

7. OpenSlide: A vendor-neutral software foundation for digital pathology.

Authors: Adam Goode; Benjamin Gilbert; Jan Harkes; Drazen Jukic; Mahadev Satyanarayanan
Journal: J Pathol Inform Date: 2013-09-27

8. Metadata management for high content screening in OMERO.

Authors: Simon Li; Sébastien Besson; Colin Blackburn; Mark Carroll; Richard K Ferguson; Helen Flynn; Kenneth Gillen; Roger Leigh; Dominik Lindner; Melissa Linkert; William J Moore; Balaji Ramalingam; Emil Rozbicki; Gabriella Rustici; Aleksandra Tarkowska; Petr Walczysko; Eleanor Williams; Chris Allan; Jean-Marie Burel; Josh Moore; Jason R Swedlow
Journal: Methods Date: 2015-10-22 Impact factor: 3.608

9. The FAIR Guiding Principles for scientific data management and stewardship.

Authors: Mark D Wilkinson; Michel Dumontier; I Jsbrand Jan Aalbersberg; Gabrielle Appleton; Myles Axton; Arie Baak; Niklas Blomberg; Jan-Willem Boiten; Luiz Bonino da Silva Santos; Philip E Bourne; Jildau Bouwman; Anthony J Brookes; Tim Clark; Mercè Crosas; Ingrid Dillo; Olivier Dumon; Scott Edmunds; Chris T Evelo; Richard Finkers; Alejandra Gonzalez-Beltran; Alasdair J G Gray; Paul Groth; Carole Goble; Jeffrey S Grethe; Jaap Heringa; Peter A C 't Hoen; Rob Hooft; Tobias Kuhn; Ruben Kok; Joost Kok; Scott J Lusher; Maryann E Martone; Albert Mons; Abel L Packer; Bengt Persson; Philippe Rocca-Serra; Marco Roos; Rene van Schaik; Susanna-Assunta Sansone; Erik Schultes; Thierry Sengstag; Ted Slater; George Strawn; Morris A Swertz; Mark Thompson; Johan van der Lei; Erik van Mulligen; Jan Velterop; Andra Waagmeester; Peter Wittenburg; Katherine Wolstencroft; Jun Zhao; Barend Mons
Journal: Sci Data Date: 2016-03-15 Impact factor: 6.444

Bringing Open Data to Whole Slide Imaging.

1. Perinodular and Intranodular Radiomic Features on Lung CT Images Distinguish Adenocarcinomas from Granulomas.

2. Proteomics. Tissue-based map of the human proteome.

3. Diagnostic Assessment of Deep Learning Algorithms for Detection of Lymph Node Metastases in Women With Breast Cancer.

4. The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging.

5. Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes.

6. Standardization in digital pathology: Supplement 145 of the DICOM standards.

7. OpenSlide: A vendor-neutral software foundation for digital pathology.

8. Metadata management for high content screening in OMERO.

9. The FAIR Guiding Principles for scientific data management and stewardship.

10. Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging.

1. A Simple Method for Creating a High-Content Microscope for Imaging Multiplexed Tissue Microarrays.

2. TissUUmaps: interactive visualization of large-scale spatial gene expression and tissue morphology data.

Review 3. Software tools and platforms in Digital Pathology: a review for clinicians and computer scientists.

4. Reference bioimaging to assess the phenotypic trait diversity of bryophytes within the family Scapaniaceae.

Review 5. Open Practices and Resources for Collaborative Digital Pathology.