Zeiss Axiovert 200 User manual

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QUICKSTART GUIDE:
WIDEFIELD 1
ZEISS AXIOVERT 200 /VOLOCITY
(SAFB 409)
Startup procedure................................................................................................................2
Adjusting brightfield Köhler illumination ...............................................................................2
Observing fluorescence through the eyepiece.....................................................................3
Acquiring images with the Improvision Volocity software.....................................................3
General informations................................................................................................................................. 3
Acquiring the image ...................................................................................................................... 3
refocussing/ re-centring: ........................................................................................................................... 3
adjusting channel presets:........................................................................................................................ 4
multidimensional acquisition setup: .......................................................................................................... 4
Shutdown procedure............................................................................................................5 
Important additional information...........................................................................................7
Volocity Video Toolbar.................................................................................................................. 7
Auto Exposure .............................................................................................................................. 8
Auto Contrast................................................................................................................................ 8
Keypad controls: ........................................................................................................................... 8
Control buttons on the lefthand side of the microscope:............................................................... 8
File formats ................................................................................................................................... 8
merge colours: .............................................................................................................................. 8
Facility for Imaging
by Light Microscopy
Observing Life As It Happens
Imperial College London

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Startup procedure
Turn on (in this order):
•if required: heater unit and heater, 4 hours before live imaging to allow focus to stabilise:
•cplate holder
•dchamber
•if required: CO2supply
•switch on the mercury fluorescence lamp
•MAIN switch on the wall, on the right side of the microscope
•computer
Log in with your local account (not your IC login) and start the Volocity software.
Adjusting brightfield Köhler illumination
•make sure the LIGHT PATH (button on the left / bottom) is switched to 100%
BINOCULAR: press button until displayed on the microscope top display
•switch to 10x objective with the objective buttons on the right side of the
microscope
•you can move your specimen in xy-direction with the joystick, holding the
button on top of the joystick makes the stage moving faster
•focus on your sample
•if focus beeps, override the top limit by pushing the top focus button on the
right side of the microscope while turning the focus wheel (when you hear double beeps, the
mechanical limit of the focus is reached which cannot be overrun)
•open brightfield shutter with S1 (labelled ‘BF’ on the filter wheel pad)
•adjust brightness with large black button on front / bottom of
microscope)
•make sure condenser iris is not completely closed (two buttons on
top of illumination filter wheel)
•completely close field iris (top silver lever) (if the image turns
completely black, reopen until you see some light, proceed to next
step and close again after you have focussed the iris)
•focus iris (black condenser focus wheel)
•centre iris (2 silver Köhler screws)
•reopen field iris until the edge is just not visible anymore

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Observing fluorescence through the eyepiece
There are 2 options to observe fluorescence: the common way would be to use the filter cubes
in the cube revolver; for some applications the use of a dichroic mirror in the filter cube position
together with the filters in the filter wheels is necessary. The latter setup will only work with the
camera, not with the eyepiece.
•make sure the excitation / emission filter wheels are in the open position,
unless needed:
•on the filter wheel pad, select FW1 and then HOME
•repeat for FW2
•with the REFLECTOR buttons choose the illumination filter (microscope,
right / bottom behind focus wheel)
•switch between brightfield and fluorescence
with FL ON / OFF (left / front / top button on
microscope)
•Æturn fluorescence immediately off if not
needed, to avoid bleaching!
•find your sample
Acquiring images with the
Improvision Volocity software
General informations
All microscope parts can be controlled by the software (shutters, filters, focus, …), except the light
path (BINOCULAR/ FRONT PORT / BASE PORT) and the objectives
Acquiring the image
•start the VOLOCITY software (make sure the dongle is attached to a USB port)
•click on the camera icon to activate the live view and microscope controls(for more information
about the Video Toolbar in the upcoming window see Additional Information section)
•on the microscope stand, change the light path to BASEPORT
•refocus/ re-centre (if needed, see "refoccussing/ re-centering")
•adjust the channel presets of the channels you need (see "adjusting channel presets")
•adjust other acquisition parameters (see "multidimensional acquisition setup")
•with a click on the camera icon on the video toolbar you capture a single frame with the
settings actually displayed in the video toolbar
•with a click on the red button icon on the video toolbar you start your recording as defined in
"Acquisition Setup"
Useful: by clicking the "Freeze" button in the software you can keep your actual live image
freezed on the screen; the acquisition stops and the shutters will close, preventing your
sample from bleaching.
refocussing/ re-centring:
ochoose the brightfield preset (preset button 1)

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orefocus/ re-centre
or
ochoose a flourescent preset
oif there is only a faint signal switch "Auto Contrast" on
orefocus/ re-centre
oswitch off "Auto Contrast"
adjusting channel presets:
ochoose a preset button for your channel settings by clicking on one
ostandard presets for filter cubes are
1 = Brightfield
2 = DAPI/ Hoechst
3 = rhodamine / TRITC/ Alexa543
4 = GFP / FITC/ Alexa488
oadjust
oexposure time, binning, gain and offset (make sure "Auto Contrast" is off!!!)
obit depth
oright click on the preset button > Overwrite
multidimensional acquisition setup:
oset multiple channels
oopen "Acquisition Setup" dialogue
otick "Change channels"
oadd as many channels as you need with the "+" button
ofrom the appearing drop down menus choose the desired channel presets
oif you don`t want to do a stack, time series or multiple positions set timepoint to 1,
choose no focus and no xy
oset stack
obefore any other adjustments: click on Z position button and set "Top" and "Bottom"
to the mechanical limits
ousing defined focus positions
move focus to mid focus plane
click on Z position button, choose "Set Zero"
move focus to top position
click on Z position button, choose "Set Top"
move focus to bottom position
click on Z position button, choose "Set Bottom"
in "Acquisition Setup" dialogue
•set "Change focus using" to "Zeiss Focus Drive"
•choose and set Z-spacing or number of slices
ousing Autofocus

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in "Acquisition Setup" dialogue
•set "Change focus using" to "Zeiss Focus Drive"
•choose and set Z-spacing or number of slices
•set "Auto-focus using" to "Zeiss Focus Drive"
•choose the lightpath where the Autofocus should take its cues from
oset time series
oin "Acquisition Setup" dialogue: set duration
oin video toolbar: set intervals
oset multiple positions
ostage needs to be calibrated for this
remove sample!!!
switch to shortest objective (10x, 2,5x or empty position)!!!
move objective turret to the lowest position!!!
choose "Calibrate Stage" from the "Stage" menu
in the "Acquisition Setup" dialogue set "Change XY using" to "Ludl XY
Stage"
o"handmade" positioning
"Video" menu > "Live Video"
"Stage" menu > "Clear All Points"
move to desired point
"Stage" menu > "Add Point"
with "Stage" menu > "Review Points" you can adjust the focus for each of
your points separately
oautomated positioning
"Video" > "XY Stage
"Stage" > "Make Well Overlay"
"Stage" > "Create Points from Well Overlay"
follow the instructions
Shutdown procedure
•check if anyone is booked after you within 2 hours
If nobody is booked within two hours:
•remove specimen
•clean oil objective lenses with lens tissue
•Important: close incubation chamber completely (Æprotects from dust)
•update time in Sharepoint
•secure your data (e.g. copy them to the server)
•shut down hardware in reverse order from startup

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If someone’s booked within two hours:
•update usage in Sharepoint
•remove your samples
•clean objective lenses with fresh lens tissue and close incubation chamber
•clear up the desk
•save files onto the server or on a mobile harddrive
•log off

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Important additional information
Volocity Video Toolbar

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Auto Exposure
•sets max pixels to 80% (not 100%) (can also be applied to a selected area)
Auto Contrast
•unlike Gain only affects appearance of the image on the screen(!!!)
Keypad controls:
•top level button 1 = transmitted light on/off (#2-4 = empty)
•FW button switches between control of:
•FW1 = excitation filter wheel (orbit excitation filters, only used for FRET or CFP+YFP)
•FW2 = emission filter wheel in front of camera, underneath microscope
Æ the orbit excitation filters must be in HOME position for use of the emission filters; if
they aren’t, press the HOME button on the external keyboard
Control buttons on the lefthand side of the microscope:
•lowest button:
•switches between frontport (empty) <> eyepiece <> baseport (camera)
•middle button:
•switches between sideport 100% (empty) <> 50/50 <> eye/ front/ base 100%
•top: Optovar in / out
File formats
•The original Volocity libraries are stored as "mvd2" files together with a folder containing the
image data in "aisf" files
•TIFF:looses all enhancements but keeps original ("raw") data
•all stacks/ channels are stored in 1 multipage TIFF with the original bit-depth (8 or 12 bit)
•TIFF for publication
•screen version of image, including colours, merge, enhancements, on-screen image
resolution, it is always 8-bit
Æ loss of original ("raw") data!!!
merge colours:
•CREATE NEW IMAGE SEQUENCE > MULTIPLE CHANNELS
•drag single channel (or z / timepoint) images onto new image sequence window