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Computer vision for microscopes

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Jan Wedekind
Jan Wedekind
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Computer Vision for Microscopes -1- Modelling Research Centre, 16th Dec 2005 Computer Vision for Microscopes Microsystem & Machine Vision Laboratory 16th Dec 2005 MMVL http://vision.eng.shu.ac.uk/mmvl/ (vision/www) MRC http://www.shu.ac.uk/research/meri/modelling_rc.html MERI http://www.shu.ac.uk/research/meri/ SHU http://www.shu.ac.uk/ Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes -2- Modelling Research Centre, 16th Dec 2005 MiCRoN European Union IST project Uppsala, Lausanne, St. Ingbert, Athens, Pisa, Barcelona, Karlsruhe project goals • Manipulate µm-sized objects • Closed-loop control of robots • 3D object recognition and tracking image acquisition • micro-camera http://wwwipr.ira.uka.de/~micron/ • microscope http://www.cordis.lu/ist/ Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes -3- Modelling Research Centre, 16th Dec 2005 MiCRoN Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes -4- Modelling Research Centre, 16th Dec 2005 MiCRoN hardware (i) camera Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes -5- Modelling Research Centre, 16th Dec 2005 test hardware (i) test environment Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes -6- Modelling Research Centre, 16th Dec 2005 MiCRoN hardware (ii) first pictures video Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes -7- Modelling Research Centre, 16th Dec 2005 test hardware (ii) microscope environment camera sensor actors Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes -8- Modelling Research Centre, 16th Dec 2005 software Mimas computer vision toolkit open source computer vision library deliver solution ⇐ restrict vision domain ⇐ develop reusable toolset • Sensor data: V4L, gstreamer-interface • Segmentation: LSI-filters, morphology, disparity-estimator, DFT, image-processing • Feature-extraction: edges, corners, ... • Feature-matching: optic flow, SVD-correspondence, correlation, champfer matching, PGH, fast POL • pose-estimation: particle filter, hough transform http://vision.eng.shu.ac.uk/mediawiki/index.php/Mimas Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes -9- Modelling Research Centre, 16th Dec 2005 Canny-like edge detector video edges Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 10 - Modelling Research Centre, 16th Dec 2005 geometric hashing 1988, Lamdan & Wolfson Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 11 - Modelling Research Centre, 16th Dec 2005 geometric hashing preprocessing recognition Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 12 - Modelling Research Centre, 16th Dec 2005 geometric hashing 2-D / 2 DOF Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 13 - Modelling Research Centre, 16th Dec 2005 geometric hashing 2-D / 2 DOF   t1     t2  = s − m 1   VM (  , m) 1 0 s 0 5 5 1 3 m m Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 14 (i) - Modelling Research Centre, 16th Dec 2005 geometric hashing 2-D / 3 DOF scene features Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 14 (ii) - Modelling Research Centre, 16th Dec 2005 geometric hashing 2-D / 3 DOF scene features hash table pose (3 DOF) misses hits 80 120 Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 14 (iii) - Modelling Research Centre, 16th Dec 2005 geometric hashing 2-D / 3 DOF scene features hash table pose (3 DOF) misses hits 80 10 120 190 Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 14 (iv) - Modelling Research Centre, 16th Dec 2005 geometric hashing 2-D / 3 DOF scene features hash table pose (3 DOF) misses hits 80 10 50 120 190 150 Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 14 (v) - Modelling Research Centre, 16th Dec 2005 geometric hashing 2-D / 3 DOF scene features hash table pose (3 DOF) misses hits 80 10 50 200∗ 120 190 150 0∗ Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 15 - Modelling Research Centre, 16th Dec 2005 geometric hashing 2-D / 3 DOF test on artificial sequence test on pipette Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 16 - Modelling Research Centre, 16th Dec 2005 geometric hashing focus stacks as model database Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 17 - Modelling Research Centre, 16th Dec 2005 geometric hashing 3-D/4 DOF test on povray sequence (time lapse) Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 18 - Modelling Research Centre, 16th Dec 2005 bounded hough transform 2001/2004, Greenspan, Shang & Jasiobedzki Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 19 - Modelling Research Centre, 16th Dec 2005 bounded hough transform 2001/2004, Greenspan, Shang & Jasiobedzki Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 20 - Modelling Research Centre, 16th Dec 2005 bounded hough transform inverse transformation Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 21 - Modelling Research Centre, 16th Dec 2005 bounded hough transform houghspace for relative shifts Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 22 - Modelling Research Centre, 16th Dec 2005 bounded hough transform focus stacks for 4 DOF Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 23 - Modelling Research Centre, 16th Dec 2005 software architecture application layers Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 24 - Modelling Research Centre, 16th Dec 2005 software architecture UML static structure Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 25 - Modelling Research Centre, 16th Dec 2005 software architecture UML collaboration diagram Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 26 - Modelling Research Centre, 16th Dec 2005 command-line tool Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 27 - Modelling Research Centre, 16th Dec 2005 tests syringe-chip video Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 28 - Modelling Research Centre, 16th Dec 2005 tests gripper video Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 29 - Modelling Research Centre, 16th Dec 2005 tests gripper2 video Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 30 - Modelling Research Centre, 16th Dec 2005 tests full automation video video Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 31 - Modelling Research Centre, 16th Dec 2005 MiCRoN setup (i) Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 32 - Modelling Research Centre, 16th Dec 2005 MiCRoN setup (ii) Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 33 - Modelling Research Centre, 16th Dec 2005 MiCRoN setup (iii) Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 34 - Modelling Research Centre, 16th Dec 2005 MiCRoN setup (iv) Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 35 - Modelling Research Centre, 16th Dec 2005 MiCRoN assembly mockup video Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 36 - Modelling Research Centre, 16th Dec 2005 MiCRoN assembly mockup video Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 37 - Modelling Research Centre, 16th Dec 2005 demonstration macro-scale demonstration Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 38 - Modelling Research Centre, 16th Dec 2005 acknowledgements • Jon Travis: technical suggestions, administrative support • Fabio Caparrelli: camera drive/electronics/driver software, electronics setup, PI driver software, management • Balasundram Amavasai: proposal, computer vision suggestions, mimas long-term strategy • Arul Selvan: students supervision, telecentric optics, shift estimation • Manuel Boissenin: realtime tracking of multiple micro-objects, parallelisation • Jan Wedekind: software architecture and integration, realtime recognition of multiple micro-objects Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 39 - Modelling Research Centre, 16th Dec 2005 Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 40 - Modelling Research Centre, 16th Dec 2005 Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 41 - Modelling Research Centre, 16th Dec 2005 Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 42 - Modelling Research Centre, 16th Dec 2005 Microsystem & Machine Vision Sheffield Hallam University Laboratory
Computer Vision for Microscopes - 43 - Modelling Research Centre, 16th Dec 2005 Happy Christmas! http://vision.eng.shu.ac.uk/mediawiki/ Upcoming: MiCRoN public final report Microsystem & Machine Vision Sheffield Hallam University Laboratory

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Computer vision for microscopes

  • 1. Computer Vision for Microscopes -1- Modelling Research Centre, 16th Dec 2005 Computer Vision for Microscopes Microsystem & Machine Vision Laboratory 16th Dec 2005 MMVL http://vision.eng.shu.ac.uk/mmvl/ (vision/www) MRC http://www.shu.ac.uk/research/meri/modelling_rc.html MERI http://www.shu.ac.uk/research/meri/ SHU http://www.shu.ac.uk/ Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 2. Computer Vision for Microscopes -2- Modelling Research Centre, 16th Dec 2005 MiCRoN European Union IST project Uppsala, Lausanne, St. Ingbert, Athens, Pisa, Barcelona, Karlsruhe project goals • Manipulate µm-sized objects • Closed-loop control of robots • 3D object recognition and tracking image acquisition • micro-camera http://wwwipr.ira.uka.de/~micron/ • microscope http://www.cordis.lu/ist/ Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 3. Computer Vision for Microscopes -3- Modelling Research Centre, 16th Dec 2005 MiCRoN Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 4. Computer Vision for Microscopes -4- Modelling Research Centre, 16th Dec 2005 MiCRoN hardware (i) camera Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 5. Computer Vision for Microscopes -5- Modelling Research Centre, 16th Dec 2005 test hardware (i) test environment Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 6. Computer Vision for Microscopes -6- Modelling Research Centre, 16th Dec 2005 MiCRoN hardware (ii) first pictures video Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 7. Computer Vision for Microscopes -7- Modelling Research Centre, 16th Dec 2005 test hardware (ii) microscope environment camera sensor actors Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 8. Computer Vision for Microscopes -8- Modelling Research Centre, 16th Dec 2005 software Mimas computer vision toolkit open source computer vision library deliver solution ⇐ restrict vision domain ⇐ develop reusable toolset • Sensor data: V4L, gstreamer-interface • Segmentation: LSI-filters, morphology, disparity-estimator, DFT, image-processing • Feature-extraction: edges, corners, ... • Feature-matching: optic flow, SVD-correspondence, correlation, champfer matching, PGH, fast POL • pose-estimation: particle filter, hough transform http://vision.eng.shu.ac.uk/mediawiki/index.php/Mimas Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 9. Computer Vision for Microscopes -9- Modelling Research Centre, 16th Dec 2005 Canny-like edge detector video edges Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 10. Computer Vision for Microscopes - 10 - Modelling Research Centre, 16th Dec 2005 geometric hashing 1988, Lamdan & Wolfson Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 11. Computer Vision for Microscopes - 11 - Modelling Research Centre, 16th Dec 2005 geometric hashing preprocessing recognition Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 12. Computer Vision for Microscopes - 12 - Modelling Research Centre, 16th Dec 2005 geometric hashing 2-D / 2 DOF Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 13. Computer Vision for Microscopes - 13 - Modelling Research Centre, 16th Dec 2005 geometric hashing 2-D / 2 DOF   t1     t2  = s − m 1   VM (  , m) 1 0 s 0 5 5 1 3 m m Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 14. Computer Vision for Microscopes - 14 (i) - Modelling Research Centre, 16th Dec 2005 geometric hashing 2-D / 3 DOF scene features Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 15. Computer Vision for Microscopes - 14 (ii) - Modelling Research Centre, 16th Dec 2005 geometric hashing 2-D / 3 DOF scene features hash table pose (3 DOF) misses hits 80 120 Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 16. Computer Vision for Microscopes - 14 (iii) - Modelling Research Centre, 16th Dec 2005 geometric hashing 2-D / 3 DOF scene features hash table pose (3 DOF) misses hits 80 10 120 190 Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 17. Computer Vision for Microscopes - 14 (iv) - Modelling Research Centre, 16th Dec 2005 geometric hashing 2-D / 3 DOF scene features hash table pose (3 DOF) misses hits 80 10 50 120 190 150 Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 18. Computer Vision for Microscopes - 14 (v) - Modelling Research Centre, 16th Dec 2005 geometric hashing 2-D / 3 DOF scene features hash table pose (3 DOF) misses hits 80 10 50 200∗ 120 190 150 0∗ Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 19. Computer Vision for Microscopes - 15 - Modelling Research Centre, 16th Dec 2005 geometric hashing 2-D / 3 DOF test on artificial sequence test on pipette Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 20. Computer Vision for Microscopes - 16 - Modelling Research Centre, 16th Dec 2005 geometric hashing focus stacks as model database Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 21. Computer Vision for Microscopes - 17 - Modelling Research Centre, 16th Dec 2005 geometric hashing 3-D/4 DOF test on povray sequence (time lapse) Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 22. Computer Vision for Microscopes - 18 - Modelling Research Centre, 16th Dec 2005 bounded hough transform 2001/2004, Greenspan, Shang & Jasiobedzki Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 23. Computer Vision for Microscopes - 19 - Modelling Research Centre, 16th Dec 2005 bounded hough transform 2001/2004, Greenspan, Shang & Jasiobedzki Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 24. Computer Vision for Microscopes - 20 - Modelling Research Centre, 16th Dec 2005 bounded hough transform inverse transformation Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 25. Computer Vision for Microscopes - 21 - Modelling Research Centre, 16th Dec 2005 bounded hough transform houghspace for relative shifts Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 26. Computer Vision for Microscopes - 22 - Modelling Research Centre, 16th Dec 2005 bounded hough transform focus stacks for 4 DOF Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 27. Computer Vision for Microscopes - 23 - Modelling Research Centre, 16th Dec 2005 software architecture application layers Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 28. Computer Vision for Microscopes - 24 - Modelling Research Centre, 16th Dec 2005 software architecture UML static structure Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 29. Computer Vision for Microscopes - 25 - Modelling Research Centre, 16th Dec 2005 software architecture UML collaboration diagram Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 30. Computer Vision for Microscopes - 26 - Modelling Research Centre, 16th Dec 2005 command-line tool Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 31. Computer Vision for Microscopes - 27 - Modelling Research Centre, 16th Dec 2005 tests syringe-chip video Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 32. Computer Vision for Microscopes - 28 - Modelling Research Centre, 16th Dec 2005 tests gripper video Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 33. Computer Vision for Microscopes - 29 - Modelling Research Centre, 16th Dec 2005 tests gripper2 video Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 34. Computer Vision for Microscopes - 30 - Modelling Research Centre, 16th Dec 2005 tests full automation video video Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 35. Computer Vision for Microscopes - 31 - Modelling Research Centre, 16th Dec 2005 MiCRoN setup (i) Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 36. Computer Vision for Microscopes - 32 - Modelling Research Centre, 16th Dec 2005 MiCRoN setup (ii) Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 37. Computer Vision for Microscopes - 33 - Modelling Research Centre, 16th Dec 2005 MiCRoN setup (iii) Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 38. Computer Vision for Microscopes - 34 - Modelling Research Centre, 16th Dec 2005 MiCRoN setup (iv) Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 39. Computer Vision for Microscopes - 35 - Modelling Research Centre, 16th Dec 2005 MiCRoN assembly mockup video Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 40. Computer Vision for Microscopes - 36 - Modelling Research Centre, 16th Dec 2005 MiCRoN assembly mockup video Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 41. Computer Vision for Microscopes - 37 - Modelling Research Centre, 16th Dec 2005 demonstration macro-scale demonstration Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 42. Computer Vision for Microscopes - 38 - Modelling Research Centre, 16th Dec 2005 acknowledgements • Jon Travis: technical suggestions, administrative support • Fabio Caparrelli: camera drive/electronics/driver software, electronics setup, PI driver software, management • Balasundram Amavasai: proposal, computer vision suggestions, mimas long-term strategy • Arul Selvan: students supervision, telecentric optics, shift estimation • Manuel Boissenin: realtime tracking of multiple micro-objects, parallelisation • Jan Wedekind: software architecture and integration, realtime recognition of multiple micro-objects Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 43. Computer Vision for Microscopes - 39 - Modelling Research Centre, 16th Dec 2005 Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 44. Computer Vision for Microscopes - 40 - Modelling Research Centre, 16th Dec 2005 Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 45. Computer Vision for Microscopes - 41 - Modelling Research Centre, 16th Dec 2005 Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 46. Computer Vision for Microscopes - 42 - Modelling Research Centre, 16th Dec 2005 Microsystem & Machine Vision Sheffield Hallam University Laboratory
  • 47. Computer Vision for Microscopes - 43 - Modelling Research Centre, 16th Dec 2005 Happy Christmas! http://vision.eng.shu.ac.uk/mediawiki/ Upcoming: MiCRoN public final report Microsystem & Machine Vision Sheffield Hallam University Laboratory