Feb 13, 2023
Insert Alignment ELYRA7
This protocol is a draft, published without a DOI.
- Rafael Camacho1
- 1Centre for Cellular Imaging, Core Facilities, Gothenburg University
- CCI_Gothenburg
Protocol Citation: Rafael Camacho 2023. Insert Alignment ELYRA7. protocols.io https://protocols.io/view/insert-alignment-elyra7-cmu4u6yw
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: January 17, 2023
Last Modified: February 13, 2023
Protocol Integer ID: 75388
Keywords: insert alignment elyra7 alignment of the stage insert, insert alignment elyra7 alignment, microscopy slide, microscopy, optical axi, stage insert, perpendicular to the optical axi, elyra7, zeiss application specialist, zeiss, slide, sample
Funders Acknowledgements:
National Microscopy Infrastructure of Sweden
Grant ID: NMIÂ (VR-RFI 2019-00217)
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Abstract
Alignment of the stage insert to ensure that the sample is perpendicular to the optical axis. This protocol is based on material provided by ZEISS' application specialists.
What is needed before to start:
- This protocol was designed for the ELYRA7
- You will need 2 microscopy slides, one of standard size and one of about 2x2cm
Troubleshooting
Turn on the microscope
Turn on the ELYRA 7
Turn on Main Switch
Turn on Components
Turn on the Microscope Computer
Note
In the ELYRA 7 if the microscope computer is not on, then the microscope's touch screen will not light up.
Open ZEN black, and choose start system
Find sample plane via the eye pieces
Note
This protocol assumes that the microscope is on, and ready for operation
ZEN black -> Locate Tab,
View of Tabs on ZEN black, top left side
and set an imaging protocol for transmitted light so you can see the sample via the eye pieces.
Microscope Control example for transmission
Software
ZEN black
NAME
ZEISS
DEVELOPER
Change the objective to the lowest magnification, typically 10X
You can change objectives in the Microscope Control panel
Prepare a clean microscopy slide having a few marker points, marker-slide. You can keep track of the surface on which you made the marks by writing TOP and DOWN
Note
The slide can be reused
Example of marker-slide used to move to find the sample plane by focusing with the low magnification objective
Place the marker-slide on the sample holder so you can focus on the appropriate sample plane
Marker-slide on the slide holder
Focus on the sample via the eye pieces
Marker spot in focus as viewed via the eye pieces
Place glasses for reflection mode
Remove the sample holder carefully and place it a side
Remove the objective lens and carefully place it a side
Prepare a clean microscopy slide of size aproximately 2x2cm
Small slide can be made by cutting a larger slide into the appropiate size
Place the 2x2cm clean glass plate on the objective turret.
Safety information
To avoid adding fingerprints to the slide you can wear protective gloves.
Make sure not to touch the cupper pin with with glass. This pin is used to read the objectives collar, and it is delicate.
Place back the sample holder (which still has on it the marker sample)
Close the imaging chamber
Acquisition Settings
Go to ZEN black -> Acquisition Tab
Set the aquisiton settings
You have settings11 steps
Load the acquisiton settings by using the Experiment Manager
In our case these settings are stored as "insert alignment"
Image Acquisition
Go to Live mode and make sure image is not saturated
Find where the fibre of the HXP is connected to the microscope body. This will be on the left hand side of the microscope's body, after the on/off button
While in Live mode, carefully take out the fibre from the HXP that is connected to microscope body until you see the sharp edges of the fibre in the field of view
Use the levelling screws of the holder to match the 2 sets of reflections to one another
Take an image snap, and save the image for your own record
Place back the HXP fibre into position so you do not see the edges of the fibre while in live view
Place objective back into the turret
Remove the sample holder carefully so you don't touch/move the levelling screws
Note
From now on be very careful of not moving the levelling screws
Remove the glass slide placed at the base of the objective port
Place back the objective
Place back the sample holder
Safety information
Be careful not to touch the levelling screws and not to hit the objective lens with the holder.