TITLE: Zeiss AxioImagerM.2 Apotome 2 Guide
AUTHORS: Condon  ND

[DESCRIPTION]
This is a training guide for the Institute for Molecular Bioscience Microscopy Core Facility's Zeiss AxioImagerM.2 Apotome 2 (Upright) microscope.

More information about the system is available here: https://imb.uq.edu.au/microscopy-fluoro-2
A video playlist of the training is also available here: https://www.youtube.com/watch?v=iJ3ae413Sqs&list=PLkGKyuSIzfzrrfy2A5_qwA5xGV9EzAFqq

[STEPS]
SECTION: System Start-up
1.   
Check the microscope to be sure it is clean. You are responsible for the condition of the microscope at the close of your session.If you find it dirty, make sure microscopy staff know about it; that is, email, phone us or by leaving feedback on the sheets provided. 
Check the eyepiece dioptre settings. If you don’t need to make an adjustment for your vision, set both to zero. Set the interpupillary distance for comfortable binocular viewing.
Log in to the computer, using your UQ-SSO credentials.
Press the (grey) power button on the bottom left hand side of the microscope stand and wait for the LCD on the microscope to finish loading.
Start the acquisition software, ZEN, by double-clicking the ZEN desktop icon.   
Please be patient: ZEN is a large program and takes a while to load and start. Double-clicking numerous times will not make this process go any faster and may, in fact, prevent it starting. Note that you may also start ZEN by right-clicking on the ZEN icon and selecting Open from the resulting menu.
If you are using a template to image specific wells, calibrate the stage position.
Objectives – always inspect and clean oil immersion objectives both before and after a session. Note only clean the objectives by using a lens wipe, do not use any solutions or solvents.
Always double check the LCD touchscreen, ZEN software or the objective itself to confirm which immersion media should be used on each objective; Dry or Oil.
Fluoro 2 has both Dry and Oil Objectives.Note:
            Dry (these never have media applied): 5x, 10x, 20x. 40x.
            Oil: 63x, 100x 
        Do not apply too much oil to the slide and objectives; one drop will suffice.Be sure to cleanthe oil off the objective between samples.Apply fresh oil for each sample.



ZEN has four basic interface screens, accessed via tabs toward the top left of the display.Locate is used when finding the object of interest through the eyepieces or via the camera system. Acquisition provides for set up of imaging provisions, and image capture.These are most used during routine imaging, and will be covered in the user tutorial.The other two screens, Processingand Analysis, provide various methods of post capture image modification and characterization, respectively.Contact microscopy staff for instruction in these functions.


SECTION: Locate Tab
2.   

This is used to focus on the sample through the eyepieces.
Ensure you remove any remaining oil from the objective or sample before changing objectives.
Select the 10x objective by clicking on the objective icon (1) in the Microscope menu on the right-hand side of the screen.
Follow the prompts if asked to change the immersion oil (2).
Place your slide on the stage. Note: the edges of the slide must be slid under the silver retention clips.
Move the eyepiece/camera slider on the right side of the microscope head into the eyepiece position (“in”).
Click on the Locate tab (3).
Select the illumination method, brightfield, DIC, or dye you wish to image, by pressing one of the favourite buttons (4) that most closely matches your own dyes emission colour.
 a.	Quad DAPI/GFP/mCherry/Cy5 are excited by individual LEDs and are detected through a quad-band emission filter, which can result in bleedthrough/crosstalk, when you can see fluorescence from a neighboring channel in the channel of interest but acquisition is fast.
 b.	BP DAPI/GFP/mCherry/Cy5 are excited by individual LEDs and are detected through individual band-pass emission filters, which results in no bleedthrough but is slower.
Using the joystick, locate a region of interest in your sample. F1 toggles the XY speed between slow and fast.
Carefully bring your sample into focus using both the course and fine focus nobs on either side of the microscope.
Switch to whichever objective you wish to use.
Move the eyepiece/camera slider on the microscope to the camera position (“out”).
Click the Live button (5), to see the live camera image on the computer display.
Click the Find Focus and Set Exposure (6) buttons to adjust the focus and exposure of the image, or adjust the exposure manually using the Exposure Time slider.
Optionally, increase the image resolution by changing the binning to 1x1 (7), then adjusting the exposure again.
If you are collecting single colour images, you may now simply click the Snap button to capture an image (8), or use the dropdown tab to capture a quick tile of your sample (9).
Click Save (10).
SECTION: Kohler Illumination
3. Close the Field Stop (two small buttons on the right-hand side along the base of the stand) and bring the image of the Field Stop into focus using the Condenser Focus Wheel (found below the stage but above the Specimen Focus Wheel).
            i.Centre the image of the Field Stop in the field of view using the sub-stage condenser centering screws.
            ii.Open the Field Stop until it is just beyond the field of view.
   2.Set the Aperture Stop to a value of three-quarters of the numerical aperture of the objective (0.75 × AN, for the               mathematically minded).

SECTION: Acquisition Tab
4. This is used to collect multicolour, z-stack or other complex multi-dimensional datasets.
 

Multicolour Images

Open the Acquisition Tab (1).
Select the type of experiment from the drop-down list (2).
Widefield Monochrome for fluorescence
Widefield Colour for brightfield and DIC images
Colour SlideScanning for fast, brightfield acquisition of whole slide (shutter open)
Apotome for optical sectioning
Select the tickboxes for the Channels you wish to image (3).
Move the eyepiece/camera slider on the microscope out to the camera position.
Click the Live button, to see the live camera image on the display (4).
Click the Find Focus and Set Exposure buttons (5) to adjust the focus and exposure for all of the Channels of the image, or manually click on each Channel to highlight it, then adjust the exposure manually using the Exposure Time  slider (6).
By default, the camera captures a 2x2 binned image. You may increase the image resolution if desired by changing      the binning to 1x1, then adjust the exposure again.
Click Snap(7) to capture a multicolour image or use the dropdown tab to capture a quick multicolour tile of your      sample.
Then clickSave.
 
Z-stacks
Perform the steps in outlined Multicolour      images above, if required.
Click on the Z-stack tickbox.
Highlight a channel with signal throughout      the sample to set the range
Now      setup the Z-stack range via one of two methods.
  5.First/Last – good for quick scans and irregular samples:
        i.Using Live view, focus up through the sample until the top is reached.
        ii.Click Set First (1).
        iii.Then, focus down through the sample until the bottom is reached.
        iv.Click Set Last (2).
        v.Select the interval (distance) between z-sections: the easiest option is to click Optimal(3). The software                     calculates the optical slice thickness and then sets the interval between slices to be less than this; ensuring that you won’t miss anything between slices.

6.Center – good for tiles scans and multi-position imaging:
        i.Bring the sample into focus.
        ii.Press the Center button (4).
        iii.Select interval (distance) between z-sections; the easiest option is to click Optimal(5).
        iv.Enter an arbitrary number of Slices (start with about 21) (6) or, alternatively, set the Range. 
7.Note: Use an odd number of slices so that the FOV you are on is included.
8.Select all of the Channels you wish to image.
9.Click the Start Experiment button (below the Live/Continuous/Snap buttons) to begin acquisition.
10.Save your data.
11.
 


SECTION: Advanced Tiling
5. Click the Tiles checkbox, situated below the z-stack checkbox mentioned previously. A Tiles parameters panel will open.
In the Tile Regions section, Show viewer (1), opens a window that allows you to define a region in Live mode (2).      
The viewer hosts all the controls to define the tiled region, as well as the ability to define individual positions for you acquisition (3). All regions to be defined with carriers are also accessible.

 
 


SECTION: Apotome
6. 2D Apotome
 
1. Carefully and gently     slide in the Apotome module, select “Apotome” from the experiment dropdown list, and select desired Channels, as described above.
2. Select Apotome from the experiment dropdown list. 
3. Check that the Apotome is Active, If there is a red X, make sure Apotome is in position. If there is a red X next to      4. Channel Calibrated, contact microscopy facility staff.
5. Select the tickboxes for Channels you wish to image.
6. Move the eyepiece/camera slider on the microscope out to the camera position.
7. Click the Live button, to see the live camera image on the display. 
        Note the Apotome blocks a lot of light and you will need to re-set exposure values when using this method.
8. Click the Find Focus and Set Exposure buttons to adjust the focus and exposure for all of the Channels of the image, or manually click on each Channel to highlight it, then adjust the exposure manually using the Exposure Time slider.
9. Increase the image resolution if desired by changing the binning to 1x1, then adjust the exposure again.

 
10. Click Snap.
Important:      In the ApoTome tab (under the image, next to the display tab), Click Create Image (1) to process the image file into a single, resolution enhanced image in the display settings area below your image.
Save your data.

3D Apotome
Carefully and gently     slide in the Apotome module, select “Apotome” from the experiment dropdown list, and select desired Channels, as described above.
Adjust exposure, resolution (if desired), and setup a z-stack as previously discussed.
Click Start Experiment.
Select Normalization (2).
Select Phase correction and set to Global bleaching to remove any lines visible in the final image (3).
Set Fourier filter to Medium (4).
Deconvolve the image (5), if desired.
Click Create Image (1), as above.
Save your data.

SECTION: Other Options
7. AutoSave enables a user to automatically save the raw .CZI files to a specified location after capture.Users should always save to the D:\Data\ directory and create a folder in their name.




AutoExport performs similarly to AutoSave but converts the raw .CZI file into the desired image format such as TIFF. (This is not recommended, and should only be used on very large tile-scans, contact facility staff for      more information)
 

Image Info,  accessed from the tabs on the left of the image window, displays all of the settings used to capture the image, including pixel size and emission wavelength.
 

SECTION: Shut Down Procedure
8. 1.Lower the stage and remove your sample
2.Cleaning up the microscope
        a.Carefully clean the oil immersion objectives, if used, using the lens tissues provided, in the manner demonstrated by the microscopy staff.Do notuse Kimwipes. If a dry (air interface) objective is oil contaminated do not attempt to clean it; notify microscopy staff.
        b.Wipe up any spills you may have made.Note well; You, the last user, are responsible for the condition of the microscope and ancillary equipment.If the equipment was found dirty, notify microscopy staff.
        c.Wipe up any shards of glass you might have produced: nobody likes being jabbed by little slivers of glass in a biology lab.


3.Make sure all of your images are saved.
4.Exit the ZEN software.
5.Transfer your files from the local computer to the network storage.
6.Log off the computer (Do not Shut down):
a    Wait sixty seconds after quitting ZEN. Microscope will automatically turn off.


Please remember that the optics on these microscopes are verydelicate, please treat the microscopes gently and with respect.Think of them not at pieces of lab equipment but as very, very expensive lenses for very specialised cameras – a really nice lens for up close work for your camera can run around $2000 and you wouldn’t grind pieces of glass into that, microscope lenses can cost much more than that and so why would you grind slides into them???