Search

Fluorescent Microscope Facility

User Guidelines

Contents

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


 

1. Training


Initial training must be undertaken if the user is unfamiliar with the Nikon Ti-E fluorescent microscope. Book a training session by filling in and submitting the registration form. Following that, please email Keren (keren.cooper@uct.ac.za) to arrange training. For detailed information, please navigate to the Facility's booking page.

 


 

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.
 


 

3 Care and Use of Equipment and Facility


3.1 H&S Requirements
For details on cleaning and disinfection of the microscope, please visit the Facility's Health and Safety page or download the information
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 and 10
1. Open My Computer/This PC
2. Select Map network drive

Acces1

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

Acces2Access3

 

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

Example:
user@host:~$ mount.cifs
–o username=wf\\0123456,password=password,rw,nounix,iocharset=utf8,file_mode=0777,
dir_mode=0777 //researchdata.uct.ac.za/MCB /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!