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Bench-Marking in 3D Electron Microscopy

Bench-Marking in 3D Electron Microscopy. ISBI Challenges. It aims to establish the state-of-the-art in microarray data analysis, as well as identify progress and highlight promising directions for future efforts. CAMDA.

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Bench-Marking in 3D Electron Microscopy

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  1. Bench-Marking in 3D ElectronMicroscopy

  2. ISBI Challenges

  3. It aims to establish the state-of-the-art in microarray data analysis, as well as identify progress and highlight promising directions for future efforts. CAMDA

  4. Every year, thousands of papers are published that describe new algorithms to be applied to medical images. But very few provide a fair and direct comparison of the newly proposed algorithm with the state of the art. We believe that such comparisons can help to substantially improve the performance of medical image analysis algorithms.Grand Challenge in Medical Imaging Analysis

  5. Toexploitthecompetitivenature of manyresearchers and drive progress forwards at a faster pace.PASCAL

  6. CHALLENGE PUBLIC DATASET

  7. Precedents

  8. http://i2pc.cnb.csic.es

  9. Instruct: TheEuropean Project tosecuretheStrategicInfrastructuresforStructuralBiology

  10. PawelPenczek (Hoston) Henning Stahlberg (Biozentrum) Michael Shatz (Image Science) SjorsScheres (MRC) RemcoSchoenmakers (FEI) John Westbrook (PDB) The Madrid I2PC team Excused participants: NikoGrigorieff (on sabbatical) ArdanPatwardhan(site visit of the EBI review panel) Holger Stark (sick) Participants AnchiCheng (San Diego) Wah Chiu (Houston) Yao Cong (Beijing) Marin van Heel (London/Netherlands) Richard Henderson (MRC) Bernard Heymann (NIH) Joachim Frank (Columbia) Robert Langlois (Columbia) Dean Leath (Albany) Steven Ludtke (Houston) Stephan Nickell (Zeiss) JuergenPlitzo (Martinsried)

  11. ParticlePicking CTF Detection 2D Alignment 2D Classification 3D Alignment 3D Reconstruction 3D Classification

  12. What are we going to measure?

  13. Data Sets for the Challenge

  14. http://i2pc.cnb.csic.es/emx

  15. Interchange Format for the CTF Challenge

  16. # EMX1.0 * # =========================================================== # .................EMX Exchange file......................... # Informationonemx file formatisavailable at # http://i2pc.cnb.csic.es/emx data_micrograph loop_ _emx_micrograph.samplingRate _emx_micrograph.defocus_U _emx_micrograph.defocus_V _emx_micrograph.astigmatism_angle _emx_micrograph.voltage _emx_micrograph.Cs _emx_micrograph.amplitude_contrast _emx_micrograph.url 2.820000 10000.000000 20000.000000 0.000000 200.000000 2.000000 0.100000 mic001.mrc 2.820000 -10000.000000 20000.000000 30.000000 200.000000 2.000000 0.100000 mic002.mrc

  17. Create an Infraestructure

  18. http://i2pc.cnb.csic.es/benchmark

  19. Goals of thispresentation • To share theconclussions of theFirst I2PC DeveloppersWorkshopwiththe GRC audience • Tocollectcommunity input on: • Theinterest of Challenges in 3DEM. Shouldwefurtherproceedwiththem? • FutureChallenges(whichonewouldyouliketoseenext?) • … so as toassurecommunitysupport and inpact

  20. You are welcome to sit on this bench • Tocollectcommunity input on: • Theinterest of Challenges in 3DEM. Shouldwefurtherproceedwiththem? • FutureChallenges (whichonewouldyouliketoseenext?)

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