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Hydrahack 1.5: Bioimaging Introduction

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Hydrahack 1.5: Bioimaging Introduction

  1. 1. Quantitative Image Analysis in the Life Sciences Simon Li someone@pitpe.co.uk 1
  2. 2. IntroductionThe use of image and dataanalysis techniques to extractquantitative information from 2D, 3D, Time-lapse, Spectralimages of biological samples. imaging Light microscopy, Confocal, Multi- photon, Electron microscopy, ...
  3. 3. IntroductionThe use of image and dataanalysis techniques to extractquantitative information from 2D, 3D, Time-lapse, Spectralimages of biological samples. imaging Light microscopy, Confocal, Multi- photon, Electron microscopy, ... Why?Traditional analysis of microscope Humans are prone to bias, and getimages is a time-consuming bored easily.manual process Biologists and clinicians haveHigh throughput (robot assisted) superior expert knowledge, and areexperiments may generate millions able to make inferences from veryof images little information
  4. 4. Some applicationsCell biology Software:Rates of cell division Opensource:Spatio-temporal protein localisation ImageJ, CellProfilerResponses of cells to new drugs R, Python, ITK, VTKLineage tracingCell motility Proprietary: Matlab, MetaMorph, Volocity, ...Disease detection and diagnosisAnalysis of tumour biopsiesRetinal blood vessel tracingCell countingAnalysis of fungal networks3D reconstructionTracing embryo development
  5. 5. Yeast strains (5000+)
  6. 6. Mitosis / cell divisionHighly choreographed process in which DNA isduplicated and a cell divides into two new cellsProblems can lead to cancer
  7. 7. Tissue culture
  8. 8. Tumour biopsies
  9. 9. Survival prediction 100 patientsMachine Learning:Random forestsPotentially predictivefeatures identified
  10. 10. Simon Lisomeone@pitpe.co.uk

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