Jun 16, 2026
Dissection scope 3NW - operation
This protocol is a draft, published without a DOI.
- 1The Francis Crick Institute
- Donald Bell: Deputy lead Crick Advanced Light Microscope STP - CALM
Protocol Citation: Donald Bell 2026. Dissection scope 3NW - operation. protocols.io https://dx.doi.org/
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: August 15, 2025
Last Modified: June 16, 2026
Protocol Integer ID: 224752
Keywords: Microscope, umanager, dissection, uEYE, fluorescent images with ueye, ueye camera of colour, ueye camera, dissection scope, fluorescent image, ueye, umanager software
Abstract
To use the uEye camera of colour and fluorescent images with uEYE and umanager software respectively.
Startup
Login to computer
Use your normal Crick short username and password
Start umanager software from desktop icon
Make sure to select the correct configuration file when prompted
MMConfig_uEyeMAN_CURRENT.cfg
(in the MM-config folder on the desktop. This will be remembered next time you login)
Select CameraMode:
Mono (greyscale for fluorescence (click on blank box below preset to see options)).
Viewing samples - Fluorescent
Select the appropriate filter set and switch ON LED source using the control pad.
This is a manual white light LED source which gets appropriately filtered by the fluorescence filters in the turret of the microscope. Select the appropriate filter manually on the microscope.
Labels reflect the Leica naming:
- GFP2 - cyan excitation light
- DSR - Green excitation light
- ET CFP - blueish excitation light
- YFP - Teal excitation light
Turn OFF LED when you don't need it.
Make sure camera is set to Mono
Acquiring images - Fluorescence
Make sure CameraMode is set to Mono and that the slider on the microscope allows light to the camera port
Open Multi-D Acq:
This will open the main panel for multi channel acquisition.
Select 'Channels' and add 'New' as appropriate.
You can select Exposure times and pseudo colouring here too.
If you want a brightfield overlay you can acquire a BF channel coloured white but you would need the transmitted rather than reflected illumination.
Select 'Save file'
- Browse to and set a sensible file saving location
- Choose single file save (one file stack for all channels)
- Enter file name
- If you wish you can also add comments which get carried in the metadata of the image
Aquire image from Multi-D Acq panel
- Turn ON LED
- You will be prompted to check the correct filter is in place before each image is acquired
- Turn OFF LED
Acquiring images - Colour -uEYE software
Make sure uManager is closed
Start the uEYE software from the icon on the desktop and choose Optimal colours (simple mode is fine).
Set up illumination appropriately using the manual settings on the microscope and/or additional external lighting.
You should remove one of the filter sets from the microscope to get a proper colour image and that the slider on the microscope allows light to the camera port.
Go 'Live' (top left icon - green)
Fit to screen (magnifier - magenta)
Adjust exposure as necessary (spanner - cyan)
Acquire an image by pressing the save button ((disk - yellow)