Quantitative Imaging, Parts I & II Spring 2014

Quantitative Imaging, Parts I & II

Obtaining quantitative data from live cell images is the key to testing mechanistic hypotheses of molecular and cellular processes. This generally requires (1) using light microscopy to probe the quantity, dynamics and/or interactions of proteins and other molecules within their native environment in the cell, and (2) using computer vision methods to analyze the acquired images and quantitatively measure dynamics and spatiotemporal regulation. For this approach to succeed, experiments must be designed such that digital images acquired with the light microscope are amenable to automated image analysis, while computer vision tools must be optimized to reliably extract complete information from the digital images as pertinent to the hypotheses being tested. 

The following two nanocourses are an introduction to using the light microscope as a quantitative instrument, from image acquisition through image analysis. Please click on the titles in order to sign up for each Part:

Quantitative Imaging Part I: Image Acquisition

Nanocourse Director: Jennifer C. Waters, Ph.D.
Curriculum Fellow: Henrike Besche, Ph.D., Henrike_besche@hms.harvard.edu

The accuracy and precision of quantitative light microscopy measurements depends on the quality of the acquired digital images.  Obtaining digital images suitable for quantitation requires careful consideration of specimen preparation, the mode of microscopy, and the optics, filters, and detector.  In Part I of this two-part course, we will (1) learn how to judge image quality; (2) discuss how the various choices of equipment and imaging parameters affect image quality; and (3) learn how to best make the compromises necessary in live cell experiments to balance image quality and acquisition speed while minimizing photo-toxicity.


First Session: Tuesday, February 18, 2014, 1:30 – 4:30 PM
Location: Building C, Cannon Room

Second Session: Wednesday, May 21, 2014, 1 - 4 pm
Location: Nikon Imaging Center


Quantitative Microscopy Part II: Image Analysis

Nanocourse Director: Hunter Elliott, Ph.D.
Curriculum Fellow: Henrike Besche, Ph.D., Henrike_besche@hms.harvard.edu

Often acquiring fluorescence images is only the first step in answering your biological question: The images contain the information you're interested in, but now how can you extract it?  We will start with the basic concepts necessary for understanding and utilizing images as data, and then survey the most commonly applied image analysis methods. Topics include segmentation, filtering, co-localization, particle detection and tracking, super-resolution methods and more. No computational or mathematical background is required, and all topics will be illustrated with easy-to-understand examples using real data.


First Session: Monday, May 19, 1 - 4 pm
Location: Building C, Cannon Room
Second Session: Tuesday, May 27, 1 - 4 pm
Location: L2-025 (Electronic Classroom, Countway Library)


Please note: These courses were designed to complement one another, and therefore students who wish to take the courses for credit are required to register for both (1 Nanocourse credit will be given for each course). The only exception are students that have taken Dr. Water’s Nanocourse on Quantitative Imaging in the past, these students may register for Dr. Hunter’s Image Analysis Nanocourse separately.

The second day will feature hands on instruction in data acquisition at the Nikon Imaging Center (3/3/14) followed by quantitative image analysis (3/5/14). Students that are interested in the second session should sign up on the website. However space is limited to 12 students and signing up on the website will not guarantee a spot in theses sessions. To be considered for the second section of this course, students should submit a statement of interest (three sentences at the most). In this statement, please say whether you have any experience with imaging (and if so, how much experience) and why you would like to take the second session for both of these nanocourses. These should be emailed to the curriculum fellow (Henrike Besche, henrike_besche@hms.harvard.edu) no later than February 4th, 2014. They will be reviewed by the course directors, Dr. Jennifer Waters and Dr. Hunter Elliott. Students will then be notified by email regarding whether or not they will be able to attend the laboratory sessions.