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Computer vision for microscopes

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Computer vision for microscopes

  1. 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 VisionSheffield Hallam University Laboratory
  2. 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 VisionSheffield Hallam University Laboratory
  3. 3. Computer Vision for Microscopes -3- Modelling Research Centre, 16th Dec 2005 MiCRoN Microsystem & Machine VisionSheffield Hallam University Laboratory
  4. 4. Computer Vision for Microscopes -4- Modelling Research Centre, 16th Dec 2005 MiCRoN hardware (i) camera Microsystem & Machine VisionSheffield Hallam University Laboratory
  5. 5. Computer Vision for Microscopes -5- Modelling Research Centre, 16th Dec 2005 test hardware (i) test environment Microsystem & Machine VisionSheffield Hallam University Laboratory
  6. 6. Computer Vision for Microscopes -6- Modelling Research Centre, 16th Dec 2005 MiCRoN hardware (ii) first pictures video Microsystem & Machine VisionSheffield Hallam University Laboratory
  7. 7. Computer Vision for Microscopes -7- Modelling Research Centre, 16th Dec 2005 test hardware (ii) microscope environment camera sensor actors Microsystem & Machine VisionSheffield Hallam University Laboratory
  8. 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 VisionSheffield Hallam University Laboratory
  9. 9. Computer Vision for Microscopes -9- Modelling Research Centre, 16th Dec 2005 Canny-like edge detector video edges Microsystem & Machine VisionSheffield Hallam University Laboratory
  10. 10. Computer Vision for Microscopes - 10 - Modelling Research Centre, 16th Dec 2005 geometric hashing 1988, Lamdan & Wolfson Microsystem & Machine VisionSheffield Hallam University Laboratory
  11. 11. Computer Vision for Microscopes - 11 - Modelling Research Centre, 16th Dec 2005 geometric hashing preprocessing recognition Microsystem & Machine VisionSheffield Hallam University Laboratory
  12. 12. Computer Vision for Microscopes - 12 - Modelling Research Centre, 16th Dec 2005 geometric hashing 2-D / 2 DOF Microsystem & Machine VisionSheffield Hallam University Laboratory
  13. 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 VisionSheffield Hallam University Laboratory
  14. 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. 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. 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. 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. 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. 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 VisionSheffield Hallam University Laboratory
  20. 20. Computer Vision for Microscopes - 16 - Modelling Research Centre, 16th Dec 2005 geometric hashing focus stacks as model database Microsystem & Machine VisionSheffield Hallam University Laboratory
  21. 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 VisionSheffield Hallam University Laboratory
  22. 22. Computer Vision for Microscopes - 18 - Modelling Research Centre, 16th Dec 2005 bounded hough transform 2001/2004, Greenspan, Shang & Jasiobedzki Microsystem & Machine VisionSheffield Hallam University Laboratory
  23. 23. Computer Vision for Microscopes - 19 - Modelling Research Centre, 16th Dec 2005 bounded hough transform 2001/2004, Greenspan, Shang & Jasiobedzki Microsystem & Machine VisionSheffield Hallam University Laboratory
  24. 24. Computer Vision for Microscopes - 20 - Modelling Research Centre, 16th Dec 2005 bounded hough transform inverse transformation Microsystem & Machine VisionSheffield Hallam University Laboratory
  25. 25. Computer Vision for Microscopes - 21 - Modelling Research Centre, 16th Dec 2005 bounded hough transform houghspace for relative shifts Microsystem & Machine VisionSheffield Hallam University Laboratory
  26. 26. Computer Vision for Microscopes - 22 - Modelling Research Centre, 16th Dec 2005 bounded hough transform focus stacks for 4 DOF Microsystem & Machine VisionSheffield Hallam University Laboratory
  27. 27. Computer Vision for Microscopes - 23 - Modelling Research Centre, 16th Dec 2005 software architecture application layers Microsystem & Machine VisionSheffield Hallam University Laboratory
  28. 28. Computer Vision for Microscopes - 24 - Modelling Research Centre, 16th Dec 2005 software architecture UML static structure Microsystem & Machine VisionSheffield Hallam University Laboratory
  29. 29. Computer Vision for Microscopes - 25 - Modelling Research Centre, 16th Dec 2005 software architecture UML collaboration diagram Microsystem & Machine VisionSheffield Hallam University Laboratory
  30. 30. Computer Vision for Microscopes - 26 - Modelling Research Centre, 16th Dec 2005 command-line tool Microsystem & Machine VisionSheffield Hallam University Laboratory
  31. 31. Computer Vision for Microscopes - 27 - Modelling Research Centre, 16th Dec 2005 tests syringe-chip video Microsystem & Machine VisionSheffield Hallam University Laboratory
  32. 32. Computer Vision for Microscopes - 28 - Modelling Research Centre, 16th Dec 2005 tests gripper video Microsystem & Machine VisionSheffield Hallam University Laboratory
  33. 33. Computer Vision for Microscopes - 29 - Modelling Research Centre, 16th Dec 2005 tests gripper2 video Microsystem & Machine VisionSheffield Hallam University Laboratory
  34. 34. Computer Vision for Microscopes - 30 - Modelling Research Centre, 16th Dec 2005 tests full automation video video Microsystem & Machine VisionSheffield Hallam University Laboratory
  35. 35. Computer Vision for Microscopes - 31 - Modelling Research Centre, 16th Dec 2005 MiCRoN setup (i) Microsystem & Machine VisionSheffield Hallam University Laboratory
  36. 36. Computer Vision for Microscopes - 32 - Modelling Research Centre, 16th Dec 2005 MiCRoN setup (ii) Microsystem & Machine VisionSheffield Hallam University Laboratory
  37. 37. Computer Vision for Microscopes - 33 - Modelling Research Centre, 16th Dec 2005 MiCRoN setup (iii) Microsystem & Machine VisionSheffield Hallam University Laboratory
  38. 38. Computer Vision for Microscopes - 34 - Modelling Research Centre, 16th Dec 2005 MiCRoN setup (iv) Microsystem & Machine VisionSheffield Hallam University Laboratory
  39. 39. Computer Vision for Microscopes - 35 - Modelling Research Centre, 16th Dec 2005 MiCRoN assembly mockup video Microsystem & Machine VisionSheffield Hallam University Laboratory
  40. 40. Computer Vision for Microscopes - 36 - Modelling Research Centre, 16th Dec 2005 MiCRoN assembly mockup video Microsystem & Machine VisionSheffield Hallam University Laboratory
  41. 41. Computer Vision for Microscopes - 37 - Modelling Research Centre, 16th Dec 2005 demonstration macro-scale demonstration Microsystem & Machine VisionSheffield Hallam University Laboratory
  42. 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 VisionSheffield Hallam University Laboratory
  43. 43. Computer Vision for Microscopes - 39 - Modelling Research Centre, 16th Dec 2005 Microsystem & Machine VisionSheffield Hallam University Laboratory
  44. 44. Computer Vision for Microscopes - 40 - Modelling Research Centre, 16th Dec 2005 Microsystem & Machine VisionSheffield Hallam University Laboratory
  45. 45. Computer Vision for Microscopes - 41 - Modelling Research Centre, 16th Dec 2005 Microsystem & Machine VisionSheffield Hallam University Laboratory
  46. 46. Computer Vision for Microscopes - 42 - Modelling Research Centre, 16th Dec 2005 Microsystem & Machine VisionSheffield Hallam University Laboratory
  47. 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 VisionSheffield Hallam University Laboratory

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