W1: Amira for Cell Biology and Multi-Modal Image Analysis

Date: May 24th, 2019, 2pm to 5pm 

Host: UBC BioImgaging Facility

Location: LSC 1410

Presenter: Alexander S. Hall, Ph.D.  (Thermo Fisher Scientific)

Sponsored by: SFR, Thermo Fisher Scientific, BioImaging Facility

Maximum: 30 participants

Cost: Free

Scope: This half-day workshop will consist of a brief presentation and hands-on exercises intended for new and existing users of Thermo Scientific™ Amira for Cell Biology Software. Amira for Cell Biology provides a comprehensive, multimodal digital lab for quickly visualizing and segmenting complex microscopy data. Researchers can automate segmentation workflows on image data in batch and export beautiful animations and statistics.

The course will highlight the important features and unique functionalities of Amira for Cell Biology such as:
·         Large Data Visualization
·         Multichannel Data
·         Time Series Data
·         Cell Tracking
·         EM and Optical Data Registration
·         Recipes for Automation

Participants will have the option to follow along using their own computer. Trial codes will be provided. Read system requirement for Amira for Cell Biology (  

Information about software distribution and installation will be e-mailed approximately one week prior to the workshop.


W2: Principles and practical correlative 3D imaging using micro-computed tomography and scanning electron microscopy with focused ion beam

Date: May 21st, 2019, 1pm to 5pm

Host: UBC Centre for High-Throughput Phenogenomics 

Location: UBC Centre for High-Throughput Phenogenomics, UBC LSC 1410

Presenters: Dr. Gethin Owen (SEM), Dr. Guobin Sun (Micro-CT), Dr. Nancy Ford (Director)

Maximum: 15 participants

Cost: $100 per participant

Scope: 3D correlative imaging with both micro-computed tomography (micro-CT) and scanning electron microscopy with focused ion beam (SEM/FIB) is a very powerful technique for investigating the ultrastructure of relatively large samples. This workshop will offer an introduction into 3D correlative imaging, combining micro-CT and SEM/FIB, and demonstrate each imaging technique to highlight their capabilities in resolving ultrastructure at different levels of resolution. 3D datasets, collected from each technique during the workshop, will be reconstructed in AMIRA to create 3D models for analysis and quantification. This workshop will be geared towards investigators who have some experience in either technique but those interested in exploring 3D correlative imaging are also welcome to attend. 


W3: Imaging processing with ImageJ/Fiji Macros

Date: May 21st, 2019, 9am to 12pm

Host:  Neuroimaging and NeuroComputation Centre @ Centre for Brain Health

Location: F103, Koerner Pavillion UBC Hospital

Presenter: Jeffrey LeDue

Maximum: 16 participants

Cost: Free

Scope: This workshop is aimed at image processing and analysis novices.  No prior knowledge of coding or experience with ImageJ will be assumed. The workshop will be divided into two parts.  In the first part, we will use a sample data set to introduce ImageJ/Fiji.  In particular, we will guide users through the process of automating image processing by taking advantage of the ImageJ macro recorder and customizing its output.  In the second part, we welcome participants to share their data and processing challenges from their own research projects.  After discussion, we will work in small groups to address these real image processing challenges using ImageJ and other suitable tools.


W4: Single-particle cryo-EM pipeline

Date: May 21st, 2019, 9am to 5pm

Host: UBC High Resolution Macromolecular Cryo-Electron Microscopy Facility

Location: High Resolution Macromolecular Cryo-Electron Microscopy Facility

Presenters: Dr. Claire Atkinson

Maximum: 12 participants

Cost: $50 per participant

Scope: This workshop is aimed at those interested in pursuing high-resolution structural studies using single-particle cryo-EM approach. Using apoferritin as a model substrate, the workshop will demostrate the different stages of the cryo-EM pipeline: vitrification, data collection, and data analysis. We will begin with a hands on practical freezing of apoferritin using the Vitrobot, and then a demonstration of clipping and grid loading into the Titan Krios transmission electron microscopy. We will then cover screening grids for ice quality and setting up data collection using the EPU package. Lastly, we will use cryosparc package to perform initial analysis of the collected images. 


W5: Super resolution microscopy workshop

Date: May 21st, 2019, 9am to 5pm

Host: UBC LSI IMAGING, Life Sciences Institute

Location: LSC Room TBA & LSI Imaging Facility

Presenters: Dr. Keng Chou (UBC Department of Chemistry and LSI IMAGING, seeing is believing, the advancement of imaging); Dr. Sheila Teves (UBC Department of Biochemistry & Molecular Biology); Madison Bolger-Munro (UBC Department of Microbiology & Immunology); Rebeca Cardim Falcao (UBC Department of Mathematics); Dr. Guang Gao (UBC Department of Cellular & Physiological Sciences and LSI IMAGING); Ismail Khater (SFU School of Computing Science).

Maximum: 12 participants

Minimum: 9 participants

Cost: $100 per participant 


Scope: The workshop will cover the principles and applications of super resolution microscopy, advice on sample preparation, imaging acquisition and analysis. Presentations in the morning session will cover the principles and applications of super resolution imaging techniques (focusing on STED, dSTORM, SIM and PALM/SPT), highlighting work at UBC’s LSI IMAGING super-resolution microscopy facility. Hands-on sessions in the afternoon will include demonstrations of our Leica SP8 3X STED, Leica SR GSD and SuperNet dSTORM imaging analysis.


Here are some highlights of this workshop:

  • A tour of LSI IMAGING
  • 2D and 3D STED analysis 
  • Deconvolution with Huygens Professional
  • Imaris analysis of 3D super resolution imaging
  • Multiple channel dSTORM imaging
  • SuperNet network analysis and machine learning of 3D dSTORM point clouds


W6: Electron microscopy for Materials Science at 4D LABS
Date: May 21st, 2019, 10am to 3pm
Host: 4D LABS at SFU
Location: 4D LABS, TASC2 7070, 8888 University Drive, Burnaby, BC, V5A 1S6
Presenters: Xin Zhang (cryo-FIB), Lis Melo (STEM-EDS), Christoph Herrmann (HIM), Nathanael Sieb (Director)

Maximum: 15 participants
Cost: Free!

Scope: This workshop will demonstrate the advanced materials analysis capabilities at 4D LABS.  We will show the cryo-FIB being used for cross-section analysis of soft materials.  Our workflows for lift-out and thinning will also be discussed.  We will demonstrate the advanced elemental analysis capability of our STEM using a lift-out sample from the FIB.  Finally, attendees will see the Helium Ion Microscope in action working with non-conducting samples.  Participants will be split into 3 groups and spend approximately 1 hour at each tool.  There will also be a general tour of the 4D LABS facility and an opportunity to see a demonstration of electron holography of semiconductor nanowires.


Attendees will need to arrange their own transportation as necessary.




W7: 3D Imaging from the Micron to the Atomic Scale

Date: May 24th, 1pm to 4pm

Location: UBC LSC 1330

Presenters: Nabil Bassim and Brian Langelier (CCEM, McMaster U)

Maximum: 30 participants

The development of advanced engineering of materials requires the ability to determine and understand their 3D structural and compositional characteristics down to the nanoscale, and beyond. Characterization at these length scales is non-trivial; however, with increased demand for knowledge in 3D at high spatial resolution, there have been developments in techniques and instrumentation that enhance research into such fine-scale features. These techniques include focused ion beam (FIB) tomography, and atom probe tomography (APT).
FIB serial sectioning tomography has the potential to bridge the gap between X-ray computed tomography (CT), with a length scale of microns, to transmission electron microscopy (TEM) tomography, at nm resolution. Since many materials properties’ hinges on their mesoscale length structure, this is a useful range of imaging. The technique consists of preparing a block face of the material using a high current ion beam, followed by ion slicing of a front face and electron-beam imaging of the newly exposed face. Repeating this slice and subsequent imaging allows the user to make up a 3D dataset. Since electron beams acquire the block face image, there is also the possibility of incorporating structural (electron backscattered diffraction) and chemical (energy dispersive X-ray spectroscopy) measurements with the imaging. This workshop will discuss critical parameters of FIB tomography such as the ion sources, information limits, sample preparation and handling complex data.
APT captures 3D structural and compositional information at the sub-nanometer scale by sequential field-evaporation of surface atoms from needle-shaped specimens. As atoms are evaporated, their position and time-of-flight are measured. From this information, an atom-by-atom 3D reconstruction can be generated, in which the original positions and elemental identities of the atoms are known. This reconstructed model allows for material analysis with high spatial resolution and excellent elemental sensitivity. While originally developed for metals, laser-pulsed APT acquisition and FIB specimen preparation techniques now allow for analysis of materials with varying conductivity and uniformity. APT is also well-suited for use with other analysis techniques (e.g. scanning TEM (STEM), electron energy loss spectroscopy), that can complement each others’ advantages and disadvantages. This workshop will cover the fundamentals of APT, and how APT can be applied to analyze nanoscale material features in complex materials. Examples of APT applications will be presented from recent research at the Canadian Centre for Electron Microscopy (CCEM).




W8: Environmental and correlative microscopy workshop

Date: May 24th, 1pm to 4pm

Location: UBC LSC 1416

Organizer: Marek Malac (Alberta U.) and Misa Hayashida (NRC)

Maximum: 30 participants

Sponsored by Hitachi High Technologies Canada


The aim of the workshop is to provide participants with examples and demonstration of the newest developments of in-situ and correlative microscopy. In-situ experiments examining samples by optical, x-ray and electron microscopes provide the tools needed to answer question posed by both fundamental science and practical applications. The workshop is divided into two segments. First, an example of exciting science investigated by in-situ electron microscopy will be presented by Prof. Jane Howe. Her talk will be followed by presentation and demonstration by Dr. Stas Dogel and Mr. Hooman Hosseinkhannazer on the recently developed MEMS devices for in-situ and correlative microscopy. In both segments, ample time will be devoted to discussion and questions.




The workshop will include hands-on demonstration of MEMS environmental TEM devices using Hitachi TM-4000 scanning electron microscope.




W9: 4D STEM and Ptychography Workshop

Date: May 21th, 2pm to 5pm

Location: UBC LSC 1510

Organizer:L Arthur Blackburn (University of Victoria), Robert McLeod (Hitachi High Technologies Canada)

Maximum: 30 participants

Sponsor: Hitachi High Technologies Canada


4D-STEM collects diffraction patterns at a series of electron beam positions, creating 4-dimensional datasets that can be processed post-collection or in a near-live condition to reveal insights into the sample material. This workshop will guide participants through the background, collection and data processing aspects of 4D-STEM, through demonstrations and hands-on walk throughs of Python based examples.


Attendees bringing their own computer will be instructed on installing and running Python modules such as Hyperspy and Pixstem for processing 4D-STEM data. Data acquisition is usually performed with vendor software, such as the Hitachi Azorus system, which will be used in this workshop for illustrative purposes. Ptychography, which can yield quantitative phase and amplitude information on the electron transmission from processing specific 4D-STEM data collected under appropriate conditions on suitable samples, will also be discussed and demonstrated.


Workshop Details []




New! W10: Beyond Spectral imaging

Date: May 24th, 2019 (afternoon)

Locaiton: F103, Koerner Pavillion UBC Hospital

Organizer: Jeffrey LeDue & Leica Microsystems

Maximum: 15 participants 

Sponsor: Leica Microsystems

Scope: In this workshop we will demonstrate the ability of microscopes to record and analyse fluorescence lifetime data in a variety of biological specimens.  This microscope features a 2P setup with spectral NDDs and a fast resonant scanner for fast imaging.  The workshop will introduce you to the curve fitting for FLIM data and phasor plots.  Lastly, we will also be talking about how to do FLIM FRET on this system.