Fluorescent Microscope Facility

User Guidelines

User Guidelines


1. Training

2. Accreditation as a microscope user

2.1 Switching on and off
2.2 Precautions when using oil
2.3 Use of Slides and coverslips
2.4 Initial scanning and focussing
2.5 Software
2.6 Disposal and removal of samples
2.7 Declaration

3. Care and use of equipment and facility

3.1 H&S Requirements
3.2 Booking
3.3 Viewing of hazardous samples
3.3 After viewing/imaging has been completed

4. Access control

5. Computers and data storage

5.1 Instructions on saving your microscope images on the Rosalind Server
5.2 Saving your image files
5.3 Viewing saved image files remotely

5.4 Using NIS Elements remotely

1. Training

Initial training must be carried out by Willem Swart. Book a training session by filling in the training form and submitting it online.



2. Accreditation as a Microscope User


You will need to pass a competency test before you can be accredited to work on the microscope independently. Arrange a time with Keren Cooper or Faezah Davids to demonstrate your ability to carry out the following instructions:


2.1 Switching on and off
a) Switch on the microscope and the lamps, and understand the function of each component.
b) Not to switch on the Intensilight (the Hg Lamp) within one hour of it being switched off
c) To switch off at the end of your session.

2.2 Precautions when using oil
a) Clean immersion oil from the lens using lens cleaning tissue without dragging the 40X objective through the oil. If this happens, you will be expected to clean that lens as well.

2.3 Use of Slides and coverslips
a) Load the slide onto the stage correctly.
b) Slides should be clean and free from excess mounting fluid.
c) Only clear varnish should be used. No glitter will be allowed.
d) Varnish must be dry before use.

2.4 Initial scanning and focussing
a) Only the 4X and 10X objectives should be used for this purpose.
b) Focussing and navigating your way around the slide.

2.5 Software
a) Find the Ti pad and the camera control pad
b) Capture an image

2.6 Disposal and removal of samples
Users must remove and dispose of all their samples in their own Labs. No disposal methods (waste bins or bottles etc.) will be provided.

2.7 Declaration
After an accreditation number has been assigned, a declaration form must be submitted before users will be granted access to the microscope.


3 Care and Use of Equipment and Facility

3.1 H&S Requirements
Users must wash their hands on entering and leaving the Microscope Facility.
Users are required to spray with 70% Ethanol where necessary and follow the guidelines for working in a BSL-2 Laboratory (link). Hand soap, paper towel and 70% Ethanol will be provided.

3.2 Booking
Microscope must be booked in advanced, using the booking form.

3.3 Viewing of hazardous samples
The microscope is located within a bio-safety level 2 (BSL-2) laboratory. If viewing live BSL-2 cells (guidelines on BSL levels can be found here), the following rules MUST be adhered to:

  • Microscope users must bring all necessary H&S consumables with them (gloves, etc). These items as well as all slides, cells and reagents must be removed after use for disposal in their own labs.
  • Cultures must be securely sealed.
  • Cultures must be transported in secondary containment.
  • The imaging process must be transient.
  • Cultures must be returned immediately to a BSL-II lab.
  • Users must have a plan of action in the unlikely event of a spill/breakage.

3.3 After viewing/imaging has been completed
Users are expected to leave the equipment in a clean state and in the proper configuration (may be useful when live imaging is being done).


4 Access control

You will be given access to the MCB Fluorescent Microscope Facility (4.32.1) and the Rosalind Server once you have past your competency test and have been accredited as a MCB Fluorescent Microscope User.


5 Computers and Data Storage

5.1 Instructions on saving your microscope images on the Rosalind Server
A specialist Server, called Rosalind, is available for you to save your microscope images remotely. This will save the microscope PC from becoming clogged up with user images and will also allow you to access your images when you get back to your laboratory. Part of your payment for the use of the microscope includes the safe storage of all your images for 6 weeks. Your data will be backed up during this period. It is your responsibility to find a solution for the storage of your images beyond this 6 week period.

5.2 Saving your image files
A folder with the day's date will automatically be created on the Rosalind Server when you activate NIS elements from the microscope computer. All image files should be saved in this folder. Any files saved to the microscope PC will be deleted. You will be able to access these files remotely from the following address:
For e.g. \\researchdata\MCB\Rosalind\01242982\20140627\..., where 01242982 is your student or staff id.

5.3 Viewing saved image files remotely
You will first have to map the Rosalind drive to your computer.
You must be logged in to the server in order to map the network drive to MCB Central Data share.

Mapping a drive to the MCB Central Data share
You have to be logged in to the server in order to map the network drive to MCB Central Data share.

Windows 7
1. Open My Computer
2. Select Map network drive


3. Next select a drive letter, e.g. O:
4. Type in the path to the folder ie. \\\MCB
5. Select the reconnect at logon to automatically remap your drive when you logon


Windows XP
1. Open My Computer --- > Map Network Drive or in Windows Explorer click on Tools | Map network drive


2. Next select a drive letter (Use O: for the data share)
3. Type in the path to the data share, ie. \\\MCB
4. Next click reconnect at logon
5. Click on "Connect using a different username" link
6. Enter your UCT network UserID & password, e.g. or wf\01234567


Use the following command to mount the CIFS share
Command Line:

user@host:~$ mount.cifs
–o username=wf\\0123456,password=password,rw,nounix,iocharset=utf8,file_mode=0777,
dir_mode=0777 // /mnt/MCB

The network drive will appear in your left hand side screen
Rt click on ROSALIND, and you will be able to map the network drive so that you can always see it when you log onto your computer. You can assign a letter for the network drive, for eg R for Rosalind!

Accessing UCT resources from off-campus
Several services and resources, such as the research data store are not available for public access via the internet. The data store is hosted in the ICTS datacentre on campus and security is managed via the UCT perimeter firewall. All external access to the data is blocked by the UCT firewall. UCT staff and students can however access this resource securely over the internet via the campus VPN solution (WEBVPN).

What functionality does it provide?

  • Web Browsing internal UCT sites
  • Browsing network drives
  • SSH & Telnet
  • Remote Desktop Services
  • VNC

1. Point your web browser to
2. Select from the Group dropdown list – WebVPN
3. Next enter your UCT staffID, or StudentID or 3rd Part ID and network password
4. To access internal UCT web sites:
5. To access your central data store, ie. cifs:// Please note the (cifs syntax from web browser)
6. Access the data store from Windows OS, ie. \\\MCB

You will be asked to authenticate using wf\staffID and network password

It will only allow access to internal UCT resources from inside the VPN browser window. For all other applications installed on your computer which require access to internal UCT resources you would need to install the Cisco AnyConnect Mobility Client (full details of this installation are available here:

5.4 Using NIS Elements remotely
We have two dongles for NIS Elements. The first dongle is installed on the microscope PC and is to be used for acquisition of images. The 2nd dongle is installed remotely on a central server. We have a license for one user at a time to access NIS elements via this dongle.

In order to gain remote access to the computer used for analysing images, you will need to make use of a VNC (Virtual Network Computing) program to share screens with that computer.

TightVNC is a free, lightweight, and fast program that will allow you to remotely access that computer, and it can be found at the following address: Download the appropriate version for your own operating system (e.g. 32-bit or 64-bit for Windows).

Run the installer. When asked to "Choose Setup Type" select "Custom." You will only need the TightVNC Viewer in order to access the computer used for analysing images, so choose to not install the TightVNC Server by selecting the X from the drop-down menu as shown in the image below. You can select whatever location you like on your hard drive to install it to.

Click "Next" and continue with the installation using the default settings from here on out. Eventually, click "Finish." TightVNC Viewer is now installed.

Run the TightVNCViewer program. In the Remote Host field, enter the following: ""

Next, click on the "Options..." button underneath "Connect," and change it to match the following for best quality. You can also change settings to match your own preferences if you so prefer.

Click the "OK" button, which will return you to the previous screen. Click the "Connect" button, to connect to the remote host (the computer for image analysis).

You will be asked to enter a Password. Enter "rosalindmcb" and press "OK"

TightVNC Viewer will now connect to the remote host and open the following screen:

You can think of the TightVNC Viewer program window almost as a virtual PC. Everything you do in that window is being fed remotely to the image analysis computer as instructions, and your PC is being fed the image from that computer's screen in return. Some multiple-key shortcuts such as Ctrl-Alt-Delete need to be sent through using the shortcuts buttons on the TightVNC Viewer window. In this case it is the three-button icon on the left hand side of the below picture, found near the top left of the Viewer window.

Mouse over these buttons to see what they do. Some of those buttons such as those that control scale and full-screen options may prove useful to you.

Now you'll be able to log in to the analysis computer remotely using the same credentials that you used on the computer in the microscope room, and you'll be able to use the image analysis software as if you were using that computer itself.

You should also have access to Rosalind (where microscopy data is stored) from the analysis computer. If you don't you can easily gain access to it by following these instructions:

  • Click the "Computer" shortcut on the desktop
  • Click "Map Network Drive" (one of the buttons near the top of the window that opens, near the middle)
  • Enter any unused Drive letter, and in the Folder field enter: "\\\MCB"

  • Click "Finish"

You should now be able to access Rosalind through the file explorer as a Network Drive with the letter you assigned it (Y: drive, in the case of the above picture).

Please log off on the analysis computer when you are done analysing your images by navigating to the start menu and clicking log off, as simply exiting the TightVNC Viewer program on your own PC will not log you off.