Unit 1: Introduction


  • Lecture 01: Welcome and Introduction [pdf]
  • Lecture 02: Mini Tour of Biology [pdf]
    Keywords: cell size & scale, tissue types, tissue organization, the animal cell, DNA, RNA, FISH, cell cycle,
  • Lecture 03: Mini Tour of Biology [pdf]
    Keyworks: proteins and their function, antibodies, labeling proteins with antibodies, green flurescent proteins, engineered organisms, cell to cell communication, basic signaling, pathways


Unit 2: Imaging Methods


  • Lecture 04: Imaging Methods [pdf]
    Keywords: microscopes, signal to noise ratio, flatfield correction, hyperspectral imaging, DIC, phase constrast imaging
  • Lecture 05: Imaging Methods
    Keywords: fluorochromes and fluorophores, quantum dots, fluorescence microscopy, toxicity, multi-spectral imaging, multi-channel imaging, photobleaching, autofluorescence, deconvolution, confocal imaging, viewing 3D images, maxium intensity projections, Raman spectroscopy


Unit 3: Image Preprocessing


  • Lecture 06: Image Preprocessing
    Keywords: representation of digital images, pixels, image statistic, cross correlation, auto-correlation, clustering
  • Lecture 07: Image Preprocessing
    Keywords: images as continuous functions, linear filters, smoothing, average filters, Gaussian filters, Fourier domain

Unit 4: Segmentation Methods

  • Lecture 08: Image Segmentation 1
    Keywords: segmentation problem, feature extraction, clustering, mean-shift segmentation, region growing
  • Lecture 09: Image Segmentation 2
    Keywords: edge detection, anisotropic diffusion, watershed segmentations, level set methods, geodesic contours, cartoon model
  • Lecture 10: Image Segmentation 3
    Keywords: connected components, basic notation for graphs, graph cut methods, normalized cut

Unit 5: Morphological Assessment of Cells

  • Lecture 11: Blob Segmentation 1
    Keywords: morphological filtering, erosion, dilation, distance transform, tesselation, Hough transform
  • Lecture 12: Blob Segmentation 2
    Keywords: circles and regularity, ellipse parameters, model based merging and splitting
  • Lecture 13: Feature Statistics
    Keywords: entropy, feature selection, classification, adaboost

Unit 6: Validation Methods

  • Lecture 14: Validation Methods
    Keywords: The concept of ground truth, annotating images, multi-observer validation, outlier detection, edit based validation

Unit 7: Tubular Structures

  • Lecture 15: Segmentation of Tubular Structures 1
    Keywords: Microvasculature, angiogenesis, neuron tracing, tracing algorithms, skeletonization
  • Lecture 16: Segmentation of Tubular Structures 2
Unit 9: Time-lapse Microscopy
  • Lecture 17: Time-lapse Microscopy 1
Keywords: Cellular motion, 5D imaging, visual tracking, data association, Hungarian algorithm, Kalman filter
  • Talk: Time-lapse Microscopy 2: Minimum-Cost Flow Cell Tracking

Unit 10: Image Registration

  • Lecture 18: Image Registration
Keywords: Kalman filter, motion, models, particle filter, tracking with level sets, lineage trees, cell cycle
  • Talk: Image Registration: Masked Object Registration in the Fourier Domain

Unit 11: Phenotyping

  • Lecture 19: Phenotyping
Keywords: Genotype, phenotype, manipulation methods, gene knockouts, RNAi screens, low-dimentional phenotypes, gene set enrichment>
Dirk Padfield,
Jan 23, 2014, 7:42 PM
Dirk Padfield,
Feb 13, 2014, 3:12 PM
Dirk Padfield,
Feb 12, 2014, 7:10 AM
Dirk Padfield,
Feb 21, 2014, 10:09 AM