NeuroTechnology Studio Training Resource

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.

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  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

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 lding@bwh.harvard.edu 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  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

Lif2Tif

Lif2Tif instruction video

 

CZI2Tif Converter

 

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

CZI2Tif

CZI2Tif instruction video

 

 

GeneralPurposeCode

 

GeneralPurposeCode list sample codes for multiple general purpose when doing macro programming, including initialization, batch process setup, parameter input and print summary table.

GeneralPuposeCode

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

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.

Measurement

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

FIJI ImageJ Educational Tutorial

 

#1:   Install FIJI ImageJ (PC)

#2:   Update FIJI ImageJ (PC)

 

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