Instrument Operation

Wide-field microscopy training (23 topics)

User beginner 36 mins 44 secs

Last updated 6 months ago

This module invites you to learn the operation of a wide-field epi-fluorescence microscope. This general training applies to a wide range of wide-field microscopes.

Introduction

Introduction

Training Series Overview
Overview of transmitted light microscopy techniques: Brightfield, Phase contrast, and Differential interference contrast
Overview of fluorescence imaging
Comparing upright and inverted microscopes
Microscope components and light paths

Starting the system

Starting the system

Starting up the microscope
Function of the Automatic Microscope Controller (AMC) unit
Control of lamps by the AMC unit
Timing of lamp use

Fluorescence lamp operation

Fluorescence lamp operation

The different lamps attached to microscopes around the facility
How to change the intensity of the light
How to illuminate your sample
How to troubleshoot

Sample mount and focus

Sample mount and focus

Mounting the sample on the microscope
Adjusting the lamp for your sample
Focusing on your sample
Focus lock
Tips on finding your sample

Objectives

Objectives

Dry objectives
Numerical aperture (NA)
Immersion objectives and immersion oils
Cleaning objectives before and after imaging
Cleaning your slide

Adjusting the eyepieces

Kohler illumination microscope adjustments

Brightfield imaging

Brightfield imaging

Adjusting the aperture stop based on your objective for contrast
Setting the microscope component for imaging
Enhancing contrast of the image

Phase contrast imaging

Phase contrast imaging

Checking you have a phase contrast objective
Choosing the correct phase ring on the condenser
Adjusting the microscope components for high contrast

Differential Interference Contrast (DIC) imaging

Differential Interference Contrast (DIC) imaging

Theory of DIC imaging
Microscope components required for DIC imaging
Examples of DIC images
DIC components that can effect fluorescence imaging

Fluorescence imaging

Fluorescence imaging

Examples of fluorescence probes
Microscope components needed for fluorescence imaging
Epifluorescence light source optimization
Troubleshooting tips

Image acquisition NIS-F elements

Image acquisition NIS-F elements

Opening the software
Camera operation
Changing viewing and acquistion resolution
Optimizing the contrast in your image
Adding and adjusting the scale bar
Autoexposure function
Focusing tips
Creating an RGB image from 3 separate images
Saving your images

Source material

Institute for Molecular Bioscience Microscopy

Zeiss Axio Imager 2 with Apotome training (24 topics)

User beginner 53 mins 52 secs

Last updated 6 months ago

This module invites you to learn the operation of Zeiss Axio Imager 2 fluorescent microscope equipped with Apotome system.

About Zeiss Axio Imager 2 with Apotome

Zeiss Axio Imager 2 is a fluorescent microscope. It is equipped with the Apotome system that allows to create optical sections resulting in resolution that is aproaching the resolution of laser scanning confocal microscopy.

System & software overview

System & software overview

Training Series Overview
Microscope and lightpath layout
Powering on the system & Starting Zen
Zen Blue Software Layout and Tabs

Finding your sample

Finding your sample

Mounting your slide & adding immersion oil
Selecting Objectives + Filters in Zen Blue
Focusing on your sample
Overview of the Locate Tab in Zeiss Zen Blue
Quad Band vs Single Band filter cube selection
Colour vs Mono camera selection
Taking a Snap and the Quick Snap Tiles

Acquiring an image

Acquiring an image

Overview of the experiment modes (Widfield Monochrome, Widefield Colour, Colour Slide Scanning & Apotome)
Overview of the Live/Snap buttons
Options for multi-dimensional imaging (Z-stacks & Tiling)
Regions/Auto-Saving/Exporing Images/Automation
Acquisition Settings
Channels Settings (Selecting channels, adjusting camera settings)
Range Indicator + Display adjustments
Capturing a multi-colour 2D snap
View options (2D, Split, Gallery, 2.5D, Profile, Measure, Metadata)
DIC and Transmitted light lamp adjusting
Navigating the stage using Zeiss Zen Blue

Saving and re-using

Saving and re-using

Recognising unsaved images
Saving files manually
Setting up Auto-Save Options
Where to save data on the microscope computer
Re-Using image settings
Closing the software and cleaning up

Z-stacks

Z-stacks

Setting up Z-stacks for Multi-Dimensional Imaging
Different Z-stack modes (First/Last, Centre)
Optimal Z-steping
Capture order (All Channels per Z-stack vs Full Z-stack per channel)
Navigating Z-stacks (Gallery, Ortho Viewer, 3D Metadata)
Quickly moving between First/Middle/Last slices
Setting up a centre Z-stack

Basic tiling & positions

Basic tiling & positions

Generating Tile Scans based on Tiles, Size & Stakes
Generating multiple positions (including verifying Z-position)
Utilising the Sample Carrier
Explaining Focus Surface
Explaining Tiling Options

Advanced tiling

Advanced tiling

Opening the Advanced Tiling wizard
Turning on Live Camera Feed vs Preview scan
Generating a Tile scan based on Stake mode
Capturing 3D Tile scan
Stitching tiles

Widefield (colour mode)

Widefield (colour mode)

Explains Colour camera utilization via left port
Selecting & Adjusting BF/DIC channel settings
Display adjustment options for RGB colour images
Example tiling set-up and capture

Colour slide scanning

Colour slide scanning

Utilising the colour camera via the left port
Limited Colour channels (BF/DIC only)
Objective swapping during Tiling mode

Apotome mode (optical sectioning)

Apotome mode (optical sectioning)

Ensuring the device is 'in' and active in Zen Blue
Setting up Channels (utilising Quand Band filter cube)
Adjusting Channel settings for Apotome
2D Apotome Acquisition example
Processing and saving Apotome Images

Lens cleaning

Lens cleaning

How to clean an upright objective lens
Cleaning tips and advice
Software shutdown procedure

Source material

Institute for Molecular Bioscience Microscopy (presented by Nicholas Gordon; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia)

Zeiss laser scanning confocal microscopy training (13 topics)

User beginner 32 mins 47 secs

Last updated 6 months ago

This module invites you to learn the operation of Zeiss LSM 710 and LSM 880 laser scanning confocal microscopes.

System, software, start-up overview

System, software, start-up overview

Training Series Overview
System Overview
Starting up the system & Starting Zen Black
Zen Black Software Layout and Tabs

Finding your sample

Finding your sample

Mouting your sample
Setting up the ocular light path
Finding focus via the eye pieces
Using Load Position to store and recal focus points

Acquiring an image

Acquiring an image

Configuring the lightpath with Smart Setup
Adjusting image parameters (number of pixels, scan speed, averaging)
Using the Zoom and FOV rotation options
Using Range Indicator and adjusting laser power and detector gain
Adjusting the pinhole

Capturing z-stacks

Capturing z-stacks

Setting up First/Last Z-stacks
Setting up Centre mode Z-stacks
Using the crop tool
Using Range Select to set up your 3D capture
Navigating 3D data-sets in Zen Black

Tiling, positions & time series

Tiling, positions & time series

Setting up a tile scan
Setting up multiple positions
Using Centre mode for multi-positions Z-stack acquisitions
Setting up time series acquisitions for live imaging

Saving, auto-saving & shutdown

Saving, auto-saving & shutdown

Manually saving acquisitions
Setting up Auto-Save
Re-using acquisition settings from previous files
Shutting down the system
Cleaning objectives

Source material

Institute for Molecular Bioscience Microscopy (presented by Nicholas Gordon; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia)

Instrument Operation modules are dedicated to hands-on operation of microscopy systems.