Fall 2023 Visual Microscopy Workshop
NTS will host Fall visual microscopy workshop focused on some basic and popular topics in the optical imaging technology, including resolution limit, confocal and practical guideline on how to achieve a “Good” image.
This workshop mixes theory, practice, imaging tips and some history stories. Whether you are new to optical imaging or already have some experience, you may find this workshop helpful to enhanced and expand your knowledge of optical imaging technology.
This workshop require registration. Please RVSP to Lai Ding lding@bwh.harvard.edu
Instructor: Lai Ding, Ph.D, NeuroTechnology Studio.
Location: Hale BTM building Conference room 10012B (all dates)
Part I “Resolution: Know the limit and how to achieve it”
Tuesday
October 3rd 1PM – 2PM
Introduce the Abbe limit formula.
How to achieve the best resolution
Live demo on difference of point scan confocal and CCD-based widefield imaging systems
Part II “Principle of Confocal Microscopy”
Tuesday
October 10th 1PM – 2PM
Introduce principle of confocal imaging.
Understanding how the modern confocal system works.
Live demo of point scan confocal.
Part III “Practical guidelines for acquiring a confocal image”
Tuesday
October 17th 1PM – 2PM
Live demo of guidelines to acquire better confocal image.
Topic covers laser setting, detector adjustment, image format, average method, avoiding crosstalk …
Part IV “Introduction of Digital Image Analysis with ImageJ”
Tuesday
October 24th 1PM – 2PM
Introduction on digital image analysis, use ImageJ to demo basic operation including background subtraction, segmentation, filtering and scale.
The NTS core provides comprehensive training and consultation services on all aspects of optical imaging research. In person one-on-one training session helps user to get familiar with basic operation on the microscope acquisition software. Training is also available on core hosted image analysis software including: Aivia 3D rendering, Huygens deconvolution and FIJI ImageJ. Consultation covers on all aspects of optical imaging research including: imaging protocol design, sample preparation, image acquisition optimization, and digital image analysis/interpretation.
For training and consultation appointment, please contact Dr. Lai Ding lding@bwh.harvard.edu.
The core also host multiple workshops and seminars on principles of optical imaging techniques and digital image analysis. All workshops and seminars are open to public.
Dr. Lai Ding works at Zeiss LSM710 confocal
Visual Microscopy Workshop Series
The contents below are slides from NeuroTechnology Studio “Visual Microscopy Workshop Series”. This workshop series is typically hold twice a year (consists around 4-5 seminars each time) and open to general public. Please email Lai Ding lding@bwh.harvard.edu if you want to be added to our email list and receive workshop announcements
“Microscopy Resolution” follows the history on how physicist/microscopist gradually understand the nature of light
and the resolution limit of a microscope. It reveals definition of Abbe limit, its formula and how to apply it. In the end, it leads to a deeper discussion on what “resolution” really means. Live demo included. Download “Microscopy Resolution” slides by clicking
“Principles of Confocal” uses an artificial data set to illustrate how confocal achieves better contract, especially in
axial direction, compare to widefiled microscopy. Live demo included. Download “Principles of Confocal” by clicking
“Super Resolution” explains the techniques applied on popular super-resolution modules. Leica STED3X is used for live demo. Download “Super Resolution – case study of STED” by clicking
Super Resolution – case study of STED
“Kohler Illumination” explores one of most important and confusing concept in optical imaging: Conjugate Planes.
Live demo on spinning disk confocal offer rare opportunity for audience to see the pinhole patterns on Yokogawa disk. Download “Conjugate Planes and Conjugate Planes” by clicking
Digital Image Analysis with ImageJ workshop
This intensive 3-day workshop taught by Dr. Lai Ding, Senior Imaging Scientist of the NeuroTechnology Studio, introduces ImageJ, its basic functions, and its macro programming capabilities. Using real imaging projects, Dr. Ding will demonstrate common image analysis tasks such as basic image processing, stack alignment, cell counting and measurement. Macro writing will be covered to demonstrate how to automate a series of ImageJ commands, to process massive datasets automatically and to store results as desired. The workshop is broken down into three sessions. Interested participants can sign up for one or more sessions depending on their interest and experience. The workshop is hosted twice a year at Countway Library, Harvard Medical School.
Day ONE “ImageJ for beginners”: basic ImageJ functions, measurement, filtering, background subtraction, cell counting, particle analysis, and ethics on image processing.
Day TWO “Advanced ImageJ”: morphology filter, thresholding methods, using ImageJ on FRAP, colocalization analysis and wound assay, working with plugins, designing image analysis protocols.
Day THREE “ImageJ Macro Programming”: introduce ImageJ macro programming language, record image process protocols as macro, batch process multiple images, user interactive features in macro, case study with sample codes.
Please email Dr. Lai Ding lding@bwh.harvard.edu to be put on our email list to received announcement of the workshop.
Dr. Lai Ding at “Digital Image Analysis with ImageJ” workshop
co-hosted by Clemson University Light Imaging Facility, Jan 2019
Dr. Lai Ding at “ImageJ Masterclass”
New England Society of Microscopy (NESM) Spring Symposium, April 2019
ImageJ Macro Code Collection
The contents below are ImageJ macro codes for individual project. Read code documentation lines first to apply. Due to website security restriction, all codes are saved as .txt files. After download, please change macroname.txt to macroname.ijm
Please email Lai Ding lding@bwh.harvard.edu if you have any questions.
Lif2Tif Converter
Lif2Tif convert all individual images in a Leica .lif file into Tiff format. Download “Lif2Tif” by clicking
CZI2Tif Converter
CZI2Tif convert all individual .CZI images in a raw data folder into Tiff format. Download “CZI2Tif” by clicking
GeneralPurposeCode
GeneralPurposeCode list sample codes for multiple general purpose when doing macro programming, including initialization, batch process setup, parameter input and print summary table.
Sholl Analysis
Sholl analysis is a method of quantitative analysis commonly used in neuronal studies to characterize the morphological characteristics of an imaged neuron. This example shows how to do Sholl analysis on a already traced neuron mask image. The zip contains three parts. A) a sample image of traced neuron, B) a collection of sample codes shows how to complete the analysis from scratch, and C) a PPT slide briefly describe the steps. This code is a result of collaboration with Juan Qu (Bradley Hyman Lab, MGH) and was showcased in the section of “Introduce to Macro Programming” in the “Digital Image Analysis with ImageJ” workshop during 2012 – 2015. The code can be easily modified to work on raw fluorescence neuron images.
Measurement
The Measurement shows a typical protocol on batch process a group of images, do cell counting and save measurement of each individual image, at the end a summary table is created showing statistics of all images. This can be used as template code for users doing batch process on cell counting. The zip file contains three parts: A) a rawdata folder contains multiple raw images, B) a collection of sample codes shows how to complete the job from scratch, and C) a PDF file explains the steps. This demo code was first taught in an ImageJ macro programming workshop co-hosted with Center of Neuroscience Research (CNR) at Tufts University, and was showcased in our “Digital Image Analysis with ImageJ” workshop in later years.
FIJI ImageJ Instruction/Education Videos
Introduction to Digital Image Analysis with ImageJ Webinar Series.
#1 Oct 27th 2020 Introduction to Digital Image Analysis with ImageJ
#2 Nov 13th 2020 Make Sense of Measurement
#3 Nov 24th 2020 Segmentation/Thresholding
ImageJ for beginners
#1 Mar 15th 2021 ImageJ for beginner I https://www.youtube.com/watch?v=F6UPmlekA5g
#2 Mar 16th 2021 ImageJ for beginner II https://www.youtube.com/watch?v=2rp4IHxSaKs
#3 Mar 22nd 2021 ImageJ for beginner III https://www.youtube.com/watch?v=-eqSYlp2Skc