Quantitative Imaging: From Acquisition to Analysis

Quantitative Imaging: From Acquisition to Analysis An annual quantitative optical microscopy course at Cold Spring Harbor Laboratory

Combining careful image acquisition with rigorous computational analysis allows extraction of quantitative data from light microscopy images that is far more informative and reproducible than what can be seen by eye. This course will focus on advanced quantitative fluorescence microscopy techniques used for imaging a range of biological specimens, from tissues to cells to single molecules. The cou

rse is designed for quantitative cell and molecular biologists, biophysicists and bioengineers. 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. Concepts Covered Include:
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..and more!

03/19/2019
Course dinner 😊
04/17/2018

Course dinner 😊

QI Class of 2018! Photo by Connie Brukin.
04/13/2018

QI Class of 2018! Photo by Connie Brukin.

Confocal imaging labs @ Cold Spring Harbor Laboratory
04/12/2018

Confocal imaging labs @ Cold Spring Harbor Laboratory

Interesting and fun lecture on fluorescent proteins from Nathan Shaner 🍒
04/08/2018

Interesting and fun lecture on fluorescent proteins from Nathan Shaner 🍒

Student Kelly Eckenrode presenting image filtering results during our daily morning discussion.
04/08/2018

Student Kelly Eckenrode presenting image filtering results during our daily morning discussion.

...the students compute.
04/08/2018

...the students compute.

..and Anna laughs...
04/07/2018

..and Anna laughs...

Digital imaging lab - measuring SNR and resolution @ Cold Spring Harbor Laboratory
04/07/2018

Digital imaging lab - measuring SNR and resolution @ Cold Spring Harbor Laboratory

Learning image formation and resolution at the bench scopes, with Anna and Talley @ Cold Spring Harbor Laboratory
04/05/2018

Learning image formation and resolution at the bench scopes, with Anna and Talley @ Cold Spring Harbor Laboratory

Binder assembly is about to commence
04/03/2018

Binder assembly is about to commence

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