"The Reverse Factory: Embedded Vision in High-Volume Laboratory Applications," a Presentation from tec-connection
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The document discusses the evolving role of imaging in high-volume laboratory applications, particularly within industries such as biomedical research, pharmaceuticals, and forensic testing. It highlights advancements in next-generation sequencing (NGS) technologies, their applications across various fields, and opportunities for cost reduction and improved performance. Additionally, it emphasizes the importance of scientific and technological trends that drive the future of laboratory automation and imaging innovations.
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Improved scientific knowledge: Nobel prizes for the lab
• The Nobel Prize in Chemistry 2008
• Osamu Shimomura, Martin Chalfie and Roger Y. Tsien†
• for the discovery & development of green fluorescent protein GFP
• New labels (antibodies, nanoparticles…)
• The Nobel Prize in Chemistry 2014
• Eric Betzig, Stefan W. Hell and William E. Moerner
• for the development of super-resolved fluorescence microscopy
• New imaging modes (Raman [1930], IR, spectroscopy…)](https://image.slidesharecdn.com/08embeddedvisionalliancevisionindustryandtechnologyforumseptember2017sila-171121190004/85/The-Reverse-Factory-Embedded-Vision-in-High-Volume-Laboratory-Applications-a-Presentation-from-tec-connection-38-320.jpg)
"The Reverse Factory: Embedded Vision in High-Volume Laboratory Applications," a Presentation from tec-connection
- 1. Page 1 The Reverse Factory Embedded Vision in High-Volume (and Value) Laboratory Applications Patrick Courtney patrick.courtney@tec-connection.com Embedded Vision Alliance Hamburg 6th September 2017 V2.6
- 2. Page 2 Information-rich image sets in the hands of users
- 3. Page 3 Fred Sanger (1918-2013) • Nobel Prize 1958 • Protein sequencing • Human insulin Image credit: MRC Laboratory of Molecular Biology
- 4. Page 4 Structure of DNA 1953 Crick and Watson Nobel 1962 Friedrich Miescher 1869
- 5. Page 5 Fred Sanger (1918-2013) • Nobel Prize #2 • DNA sequencing 1980 1st generation sequencing C T G A Image credit: MRC Laboratory of Molecular Biology separationbyelectricfield
- 6. Page 6 Synopsis • Motivation: the need and the market • Laboratory as a factory in reverse • Enabled by science and technology (including imaging) • Big applications today: NGS case study • End applications: ourselves and our world, family, food • How it works: chemistry, optics, software • Role of imaging in delivering performance • Improvement curve: Carlson’s curve and what this means • Cost, speed, growing the market, new applications • The next applications for imaging • Scientific & technological trends • There are still plenty of opportunities
- 7. Page 7 Laboratory as a factory in reverse: from sample to information petrochemicals Industrial biomedical research pharmaceutical forensics environmental materials research food & drink consumer goods from well behaved to heterogenous; from solid into liquid form clinical Life sciences Physical sciences
- 8. Page 8 petrochemicals Industrial biomedical research pharmaceutical forensics materials research food & drink consumer goods clinical Life sciences Physical sciences Pharma R&D $50bn Clinical Testing $60bn Lab instruments $40bn forensic testing $20bn food testing $11bn environmental Increasing use of imaging Laboratory as a factory in reverse: from sample to information
- 9. Page 9 Clinical applications of genomics • Screening • Diagnosis • for cancer, infection • Treatment • for selection, progress, follow up • example: breast cancer BRCA1 • Emerging area • counselling and reproduction cisncancer pharmainfo.net
- 10. Page 10 Applications expanding beyond medicine • Next generation sequencing is now used very widely • Family • Food • Flu • Forensics • Fish • High volume applications of NGS: all that touches on life
- 11. Page 11 Family: self, ancestry, genealogy • Self • Inheritance • Health risk? • Regulation • FDA and terms of use • (and our pets) consumer goods
- 12. Page 12 Flu: Tracing infection Zika 2016 • 4-40 entry points from April Grubaugh, Nathan D., et al. "Genomic epidemiology reveals multiple introductions of Zika virus into the United States." Nature (2017) 546, pp401-405.
- 13. Page 13 Aircraft safety: bird strike data - what when and why Lapwing Kestrel Galah environmental
- 14. Page 14 Elements of an NGS (next generation) system • DNA strand • Flow cell • Chemistry • Optics • Laser • Camera • Software https://www.youtube.com/watch?v=9YxExTSwgPM sequencing 5min https://www.youtube.com/watch?v=pfZp5Vgsbw0 flow cell 2min illumina
- 15. Page 15 Role of imaging: the flow cell Each image 3-4Mp, 120k images per 36 cycle run = 350Gb
- 16. Page 16 Role of imaging: the optical path illumina fluorescence
- 17. Page 17 Role of imaging: how it works 8 lanes x 100 tiles. 70bp -> 28k images / lane 300k clusters per tile. 3Gb totalillumina
- 18. Page 18 Information-rich image sets in the hands of users
- 19. Page 19 Further improvements (1) Problem: 4 colour channels per image illumina
- 20. Page 20 Further improvements (1) Problem: 4 colour channels per image Solution: from 4 channels to 2 channels illumina
- 21. Page 21 Further improvements (1) Leads to other problems • But …. 2 colour chemistry can overcall high confidence G bases The sequence below shows this effect: @1:11101:2930:2211 1:N:0 ATTTATTATTAATTAAATATTAATAATAAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTAGCGCGTATGCCGTCGTCGGCGTGCAAAAAAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG +AAAAAEEEEEEEEEEEE6EEEEEAEEEEEEEEEA/EE<EEEAEE/EAEEAEEEE6</EEEEEA/<//<///A/A//////</E<//////E///A/</A/<<A////A/E<EEEEEEEAEEE/EEEAEAEAEAE6/AEAEE<AAEAEE It’s easier to see if you visualise the quality scores for this sequence single_seq_quality https://sequencing.qcfail.com/articles/illumina-2-colour-chemistry-can-overcall-high-confidence-g-bases/
- 22. Page 22 Further improvements (2) Problem: cluster density issues • Cluster density can be demanding • Especially for some samples Krueger F, Andrews SR, Osborne CS (2011) Large Scale Loss of Data in Low-Diversity Illumina Sequencing Libraries Can Be Recovered by Deferred Cluster Calling. PLOS ONE 6(1): e16607. https://doi.org/10.1371/journal.pone.0016607
- 23. Page 23 Further improvements (2) Solution: patterned flow cells 50nm spots spacing 250nmillumina
- 24. Page 24 Further improvements (2) Solution: patterned flow cells • From random spots to fixed positions • Simplification of analysis • Increase in density and reliability • So more data in less time, cost illumina
- 25. Page 25 Further improvements (3) Problem: better use of flow cell • Solution: use two surface imaging • Challenging imaging and focussing • End up with an optical head with 6 linear cameras Illumina US8143599
- 26. Page 26 Nature 507, 294–295 (20 March 2014) Improvement: Carlson’s curve and what this means
- 27. Page 27 Improvement: Carlson’s curve and what this means • average of 5x in 2 year (2.4x faster than Moore) • with a peak of 1000x in 2 years • 100k x better over 14 years vs 34 years Ben Moore, in gnuplot by grendel|khan. - Own work, Public Domain, https://commons.wikimedia.org/w/index.php?curid=31006154 Illumina Hiseq2000s BGI Hong Kong (128 units) Moore’s Carlson’s 2001 peak Carlson • Enabled by many technologies 100k is 57 and 217
- 28. Page 28 Or put it another way, if computing had improved as fast…. IBM PC XT 1983 = 34 years ago So for the technology we have now the IBM PC would have been introduced in 2003 The same year of Nemo… ….or a car would cost €0.20… or a $1000 flight, 1 cent
- 29. Page 29 Market size and trends • Lab instruments market • $40bn (instruments/service) • Segments and growth rate • Oncology, infection, reproduction, agriculture, forensic, consumer • Currently $3bn growing 30% CAGR to $12bn by 2022 • Market capitalisation: • illumina (cap $28bn) make profit of $1.7bn on sales of $2.5bn • Learnings for the vision supply chain: • Rewards fall to the users, and system integrator • Components suppliers get small % units sales • Driver: cost per genome, not raw speed • But someone has to learn the application and design the system Grand view research; Macquarie (USA) Research 2014 Consumer genomics Agri-genomics Forensics Metagenomics, drug development Immune system monitoring Reproductive health Clinical Investigation Oncology
- 30. Page 30 Market trends and remaining opportunity • Remaining potential for clinical applications • On the cost reduction from $3.000M to $1000 • Moving WGS (Whole Genome Sequencing) into the doctors practice • How many units? How many physicians? 10M • Remaining potential for all other applications • How much DNA is there out there?
- 31. Page 31 The next generation: Oxford nanopore
- 32. Page 32 What’s next? Following the trends
- 33. Page 33 Scientific and technological trends • New science: Nobel prizes • New imaging modes • New labels • New technology • Sensors • Optics • Algorithms • Robotics • Drivers: faster, easy to use, more specific, sensitive, robust
- 34. Page 34 Scientific and technological trends • New science: Nobel prizes • New imaging modes • New labels • New technology • Sensors • Optics • Algorithms Evolution of the microscope • Robotics • Drivers: faster, easy to use, more specific, sensitive, robust
- 35. Page 35 Evolution of the microscope since c.1670 Expanding the market • Drivers: quality, productivity by ease of use and automation modern microscope imaging plate readervan Leeuwenhoek benchtop microscope Individual cells: fluorescence brightfield foldscope plate of cells
- 36. Page 36 Automated cell counters: from $60k to $5k Expanding the market Beckmann, Invitrogen, SigmaAldrich automated manual
- 37. Page 37 Scientific and technological trends • New science: Nobel prizes • New imaging modes • New labels • New technology • Sensors, Optics • Algorithms • Robotics • Drivers: faster, easy to use, more specific, sensitive, robust
- 38. Page 38 Improved scientific knowledge: Nobel prizes for the lab • The Nobel Prize in Chemistry 2008 • Osamu Shimomura, Martin Chalfie and Roger Y. Tsien† • for the discovery & development of green fluorescent protein GFP • New labels (antibodies, nanoparticles…) • The Nobel Prize in Chemistry 2014 • Eric Betzig, Stefan W. Hell and William E. Moerner • for the development of super-resolved fluorescence microscopy • New imaging modes (Raman [1930], IR, spectroscopy…)
- 39. Page 39 What is the resolution revolution ? and why imaging is (still) important
- 40. Page 40 What is the resolution revolution ? and why imaging is (still) important Ernst Abbe stated a limit on resolving power (1873) By Daniel Mietchen - Own work, CC0, https://commons.wikimedia.org/w/index.php?curid=35168637 Abbe’s diffraction limit (credit: Johan Jarnestad /The Royal Swedish Academy of Sciences)
- 41. Page 41 What is the resolution revolution ? and why imaging is (still) important Ernst Abbe stated a limit on resolving power (1873) By Daniel Mietchen - Own work, CC0, https://commons.wikimedia.org/w/index.php?curid=35168637 Abbe’s diffraction limit (credit: Johan Jarnestad /The Royal Swedish Academy of Sciences) Resolution scheme: adopted from Thorley et al., Super-resolution Microscopy: A Comparison of Commercially Available Options, Fluorescence Microscopy Super-Resolution and Other Novel Techniques, Academic Press, 2014
- 42. Page 42 Super-resolution: breaking the Abbe limit Betzig et al., Science, 2006, 313, 1642-1645 to 20nm to 50nm
- 43. Page 43 Super-resolution: how it works (1) http://zeiss-campus.magnet.fsu.edu/articles/superresolution/palm/practicalaspects.html
- 44. Page 44 New reagents: Brainbow labelling and why imaging is (still) important Lichtman et al., Nature Reviews Neuroscience 2008
- 45. Page 45 Building brainbow from fluorescent proteins • Motivation: to map all the connections in the brain • What this means for the imaging supply chain: • better faster smarter cameras • multichannel, multifocal xyz-t-λ Lawson Kurtz et al. / Duke University
- 46. Page 46 Scientific and technological trends • New science: Nobel prizes • New imaging modes • New reagents • New technology • Sensors, optics • Algorithms • Robotics • Lab environment • Drivers: faster, easy to use, more specific, sensitive, robust multiple sensors AndrewAlliance
- 47. Page 47 Smartlab at LabVolution Hannover, May 2017
- 48. Page 48 What the lab really looks like: it’s a messy place A long way from lean processes, from industry 4.0 If the DNA is the ”job description for the cell”, this is what actually happens when it meets the world Cancer research makes for a messy bench. … @WorldwideCancer
- 49. Page 49 Applications tomorrow: watching the lab • Klavins Lab • “Aquarium” • See TEDx talk on synthetic “programming” biology https://www.youtube.com/watch?v=jL0cG4NJGd4
- 50. Page 50 Actions on future applications • Future imaging (super-microscopes) • Lab (factory) of the future: 20-100 cameras per lab • Hospital of the future: role of imaging in the lab • Take home message: • imaging has proven value but still only present at a very low level • Role of EU programmes
- 51. Page 53 Bringing it all together: The Healthcare Lighthouse vision Laboratory Care Surgery Rehabilitation euRobotics topic groups on medical and laboratory robotics
- 52. Acknowledgements • Almost too many to mention, but I’ll try – DNA sequencing: Illumina, HPA, Qiagen – Microscopy: PerkinElmer, Sartorius, Stefan Hell – Cell counting: Luna, Roche, Jenoptik – Smartlab: Deutsche Messe – AndrewAlliance, EU, euRobotics
- 53. backup
- 54. Page 58 How much DNA is there out there? 6x1030 microbes on earth
- 55. Page 60 Ebola and the most expensive tent in the world Dr Sam Collins Prof Ian Goodfellowactually an ion torrent machine
- 56. Page 61 Super-resolution: how it works (1) http://zeiss-campus.magnet.fsu.edu/articles/superresolution/palm/practicalaspects.html
- 57. Page 62 Super-resolution: how it works (2) Localisation is more precise than resolving In effect: trade time for space Role of imaging Actually, several techniques http://www.practicallyscience.com/category/bio/cellbio/