NeuroTechnology Studio Training Resource

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


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


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


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


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


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


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.

laiding at microscope

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 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

Microsocpy Resolution


“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

Principles of Confocal


“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

Kohler Illumination and Conjugate Planes

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 to be put on our email list to received announcement of the workshop.

laiding clemson

Dr. Lai Ding at  “Digital Image Analysis with ImageJ” workshop

co-hosted by Clemson University Light Imaging Facility, Jan 2019

laiding NESM

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 if you have any questions.



Lif2Tif Converter


Lif2Tif convert all individual images in a Leica .lif file into Tiff format. Download “Lif2Tif” by clicking


Lif2Tif instruction video


CZI2Tif Converter


CZI2Tif convert all individual .CZI images in a raw data folder into Tiff format. Download “CZI2Tif” by clicking


CZI2Tif instruction video





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.

Sholl Analysis



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


#2 Mar 16th 2021   ImageJ for beginner II


#3 Mar 22nd 2021   ImageJ for beginner III

FIJI ImageJ Educational Tutorial


#1:   Install FIJI ImageJ (PC)

#2:   Update FIJI ImageJ (PC)