Microscope manuals
How to use our microscopes
Nikon Widefield
Basic use
This protocol covers the basics of mounting your sample on the microscope and setting up the perf...
Moving the sample
The microscope contains a motorized stage which moves the sample. The stage is controlled using t...
Using the Perfect Focus System (PFS)
The perfect focus system locates the coverslip and continually adjusts the objective height to fo...
Using Live View
In live view, the microscope will continuously acquire images, allowing you to preview settings a...
Changing the optical configuration
The following sections describe the different settings that can be changed for each channel. Thes...
Adjusting the lookup tables
When acquiring images, the camera records the intensity of light falling on each pixel. This resu...
Acquiring a single image
This protocol explains how to take a simple image with just a single frame and a single channel. ...
Using the ND acquisition panel
This page describes how to use the ND acquisition panel to set up more complex imaging, including...
Cleaning up
It is important that you clean up after yourself after using the microscope, as well as transferr...
Nikon Widefield - Specifications
General Information Microscope type: WidefieldPurpose: Rapid and long-term 2D imagingFPbase link...
Online learning resources by Nikon
Nikon is now offering learning resources available online. To request a login password, please em...
Nikon Widefield - Other documents
Please, see the following PDF for additional functions on the Nikon Widefield: Manual to use ...
Nikon Spinning Disk Confocal
Nikon SDC - Basic set-up
This protocol covers the basics of turning on the microscope, mounting your sample, and acquiri...
Nikon SDC - Mode of operation
This microscope offers several capabilities, it has two light sources and one camera. In additi...
Nikon SDC - Shut-down and clean up
When you are done imaging, remove your sample from the microscope and place it on a kimwipe or ...
Nikon SDC - Specifications
General Information Microscope type: Spinning disk confocalPurpose: Rapid 2D and 3D imagingFPb...
Using the Perfect Focus System (PFS)
The perfect focus system locates the coverslip and continually adjusts the objective height to ...
Online learning resources by Nikon
Nikon is now offering learning resources available online. To request a login password, please ...
Oil Objective Tutorial Videos
Nikon A1R Laser Scanning Confocal
Nikon A1R - Overview
Basics of laser scanning confocal A laser scanning confocal microscope produces high resolution ...
Nikon A1R - Basic setup
This guide describes how to turn on the microscope and mount your sample on the microscope. If...
Nikon A1R - Moving the sample
The microscope contains a motorized stage which moves the sample. The stage is controlled using t...
Nikon A1R - Mode of operation
Overview of the OC (Optical Configuration) control panel The OC Panel contains the different li...
Shut Down and clean up procedures
When you are done imaging, remove your sample from the microscope and place it on a kimwipe or ot...
Using the Perfect Focus System (PFS)
The perfect focus system locates the coverslip and continually adjusts the objective height to fo...
Online learning resources by Nikon
Nikon is now offering learning resources available online. To request a login password, please em...
Nikon A1R - Specifications
General information Microscope type: Laser scanning confocalPurpose: 2D and 3D images of fixed a...
Nikon N-STORM
Nikon N-STORM - Startup and basic set-up
Getting the system ready Startup procedure 1. Turn on the Laser Power Strip (1). Turn on t...
Nikon N-STORM - Mode of operation
Microscope controls To control the microscope stage, you will use the joystick. The central knob...
Nikon N-STORM - Shutdown and clean up
When you are done imaging, remove your sample from the microscope and place it on a kimwipe or ot...
Nikon N-STORM - Specifications
General information Microscope type: TIRF and super resolutionPurpose: STORM- or PALM-based supe...
Using the Perfect Focus System (PFS)
The perfect focus system locates the coverslip and continually adjusts the objective height to fo...
Online learning resources by Nikon
Nikon is now offering learning resources available online. To request a login password, please em...
PerkinElmer Opera Phenix
PerkinElmer Opera Phenix - Specifications
General information Microscope type: Spinning disk confocal and widefieldPurpose: High-throughpu...
Exporting a video file
This document explains how to export a video file from a time-lapse dataset. Click on a well i...
Exporting and deleting files
After your session, you should backup your data from the Opera Phenix. There are two main file fo...
PerkinElmer Opera Phenix manual
Please, see the following PDFs for the Opera Phenix manual: Manual to adjust imaging settings ...
Analysis Workstations
Imaris Workstation Specifications
Workstation Imaris Device Name BIOF-IMAG-AYLS Processor AMD Ryzen Thread...
Elements Workstation Specifications
History The Elements Workstation has been retired. When it was running, the specifications were ...
Harmony and Aivia Workstation
Workstation Harmony and Aivia Device Name Imaging-SC2017 Processor Intel...
Bruker TruLive3D
Training manual for the Bruker TruLive3D Light Sheet Microscope. Acknowledging the Arnold & Ma...
Bruker TruLive3D training protocol
Training Program Bruker TruLive3D Light Sheet Microscope Session 1 – Instrument and Operat...
Bruker TruLive3D specifications and primary uses
Bruker TruLive3D main specifications The TruLive3D has 4 imaging channels at 405nm, 488nm, 561...
1. Bruker TruLive3D start-up procedure
a. Turn on the microscope In case of emergency, push the big red button: it turns off ...
2. Bruker TruLive3D microscope overview
a. The Bruker TruLive3D is a dual sided illumination light sheet microscope. The dual light she...
3. Bruker TruLive3D Lux-Bundle overview
Once the microscope, cameras and temperature controller and gas mixer are on it is time to op...
4. Bruker Trulive3D calibration
Calibration of the laser beams is critical for optimal imaging and should be done prior to ever...
5. Bruker TruLive3D Finding the sample
Make sure you performed the calibration of the system before lowering your sample in the chambe...
6. Bruker TruLive3D Experiment
This page will guide through the steps to set-up a basic experiment. 1. Setting up an experime...
7. Bruker TruLive3D Data management
Data acquired on the Bruker TrLive3D will typically be very large, on the order of TeraBytes of...
8. Bruker TruLive3D Using the photo-manipulation (PM) feature
The Bruker TruLive3D has a photo-manipulation (PM) feature that you can use to ablate specific ...
9. Bruker TruLive3D shut-down procedure
Once you are done with your experiment, please proceed with the following shut-down procedure: ...
Bruker TruLive3D Sample preparation guidelines
This page contains some tips for sample preparation for the Bruker Trulive 3D. It is not exhausti...
Bruker TruLive3D emission filters and fluorophores spectrum
This page will help you select which filter combination you need for most commonly used fluorop...
Bruker TruLive3D Data management pipeline
Bruker TruLive3D Data visualization in Fiji
The data generated by the Bruker TruLive3D contains a Fiji header named bdv.h5. Fiji is an open...
Microscopy Essentials
Essentials about cameras, filter cubes and more
Single Objective Light Sheet Microscope (OPM)
Oblique Plane Microscope (OPM) Acknowledging the Arnold & Mabel Beckman Foundation for their s...
Specifications and primary uses of the OPM
Single Objective Light Sheet Microscope The Single Objective Light Sheet Microscope is also re...
Using the OPM
The Single Objective Light Sheet Microscope is a custom-designed microscope and is a VERY sensiti...
Sample preparation for the OPM
Good news: Traditional sample preparation! The OPM sample holders are similar to that of other c...
Setting up an experiment on the OPM
This page is a guide to set-up an experiment with the OPM. All experiments on the OPM will be d...
OPM Data processing in Fiji
OPM Data The data generated by the OPM is in TIFF format. Whether you acquire a single image o...
Evident VS200 Slide Scanner
VS200 - Specifications
General information Microscope type: Widefield slide scannerPurpose: Rapid semi-automated scanni...
VS200 - Manual
Batch importing slide names and information Slide names and information can be imported from a C...
Evident VS200 Data Management Protocol
DATADRIVE1 (D:): The drive for active data acquisitions DATASTORAGE (F:): Temporary storage loca...
Nikon AXR and NSPARC Laser Scanning Confocals
Nikon AXR - Specifications
General information Microscope type: Laser scanning confocalPurpose: High quality 2D and 3D imag...
Nikon NSPARC - Specifications
General information Microscope type: Laser scanning confocalPurpose: High quality 2D and 3D imag...
Nikon AXR FRAP procedure
This page is a brief introduction to doing FRAP experiments with the Nikon AXR or Nikon AXR NSPAR...