Quantitative Imaging: From Acquisition to Analysis

QI is an annual two-week intensive course at Cold Spring Harbor Laboratory that is focused (pun intended!) on advanced quantitative fluorescence microscopy techniques used for imaging a range of biological specimens, from tissues to cells to single molecules. The course is designed for cell and molecular biologists, biophysicists and bioengineers looking to learn quantitative imaging approaches.

We provide a thorough treatment of the complete process of quantitative imaging, from the photons emitted from the sample to the extraction of biologically meaningful measurements from digital images. Material is covered in lectures, discussion groups and hands-on quantitative exercises using commercial microscopes and open-source image analysis tools.

Course dates: March 24 – April 7, 2020

Application deadline: January 31, 2020

Applications for QI 2020 are due in...

Why choose QI?

  • We (the course organizers) are core facility imaging scientists from Harvard Medical School who have tons of experience teaching microscopy
  • We have seminars and lectures from rockstar PIs who are making important contributions to imaging AND are excellent, enthusiastic teachers
  • We only accept 16 students, so we can maintain high faculty:student and microscope:student ratios
  • We have a strong emphasis on quantitation and modern image analysis methods
  • Confocal, TIRF, super-res & light sheets: we have all kinds of scopes, and you get to play with them
  • QI was co-founded by Jennifer Waters & Torsten Wittmann in 2011. Jennifer taught in the AQLM course at the MBL for 9 years before she was invited by CSHL to establish QI. She has developed and taught many courses and workshops over her 18 years teaching microscopy at Harvard.

We teach you:

  • Widefield fluorescence microscopy
  • Laser scanning and spinning disk confocal microscopy
  • CCD, EM-CCD & sCMOS cameras
  • Total internal fluorescence microscopy (TIRF)
  • Light sheet microscopy
  • Super-resolution microscopy (structured illumination, STED & localization microscopy)
  • Imaging and analyzing ratiometric “biosensors” (including FRET)
  • Fluorescent proteins and live sample imaging
  • Image processing (filtering, de-noising, corrections, deconvolution)
  • Image segmentation
  • Quantitative shape and intensity measurements
  • Object detection and tracking
  • Machine learning
  • Designing and troubleshooting quantitative imaging experiments

QI Organizers / Instructors

The QI Organizers/Instructors develop the course content, give the majority of the educational lectures in the course, and invite/host the speakers listed in the next session. Instructors are there for the entire course.

Jennifer Waters, PhD
Jennifer Waters, PhDMicroscopy Director & Lecturer in Cell Biology at Harvard Medical School
Jennifer directs microscopy cores, and teaches microscopy courses and workshops. She is passionate about teaching microscopy, and is obsessed with microscopes (as evidenced by her point spread function tattoo).
Talley Lambert, PhD
Talley Lambert, PhDAssociate Director of Imaging Technology & Lecturer in Systems Biology at Harvard Medical School
Talley advises and assists core facility users with advanced imaging applications, such as light sheet and super-res, and teaches in microscopy courses and workshops. Talley resides primarily in Fourier space.
Hunter Elliott, PhD
Hunter Elliott, PhDDirector of Machine Learning Research at PathAI
Hunter develops machine learning approaches to biomedical image analysis. Hunter is a computational scientist who also speaks biology.

QI Laboratory Director

Lab exercises are a critical component of QI, and Anna makes it all happen.

Anna Jost, PhD
Anna Jost, PhDAssociate Director of Imaging Education and Lecturer in Cell Biology, Harvard Medical School

QI Co-Instructors

The QI Co-Instructors give both educational lectures and seminars. They’re around for ~half the course.

Florian Jug, PhD
Florian Jug, PhDMPI-CBG Group Leader
Suliana Manley, PhD
Suliana Manley, PhDProfessor at EPFL (École polytechnique fédérale de Lausanne)

Our awesome TAs:

Under the fearless leadership of Anna, the QI TAs help develop, test and teach the laboratory exercises, and prepare all the samples. They are all awesome imaging scientists and teachers.

Check out all the fun we have!