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1. The Nanoimager has no eyepieces so focusing must be done using a camera image. This can be done using sample fluorescence, but I’ve found that it is a lot easier to use the focus laser, which reflects at the glass/water interface of the specimen and forms an image of a spot on the focus camera. The Focus Camera view is on the left of the NimOS GUI. You will just see camera noise unless the focus laser is switched on.
   
   
   

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   If the focus camera view is not visible, select Show Focus Camera View from the Instrument menu.

2. Click the Focus Laser button in the Light Control area on the right.
   
   
   

3. You will probably initially see a faint diffuse signal at the top of the focus camera view. This is what the camera view looks like when out of focus. Change the Z position in the Position Control area on the right-hand side of the screen until there is an image of a small laser spot in the focus camera view. Type -300 into the Z field and gradually increase the value (making it more positive) until the laser spot comes into focus. The correct position is when the laser spot is at its smallest and brightest.
   

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   The 'in focus' position will be different for different imaging vessels. I have found that I can get close to the correct focus with a value of about - 250 to -300 for ibidi µ-slides and +16 for the bead channel alignment slide. The latter is larger because the coverslip is mounted on spacers so the stage has to be moved to a higher position.

4. You can prevent the focus drifting by locking it to the laser reflection position. Click the Set Focus Ref. button in Position Control. The Nanoimager will auto focus on the focus laser reflection. When the auto focus is complete, click the Z Lock button to prevent further drift.
   
5. Note that the fluorescence from your specimen will most likely be at a different height to the reflection of the focus laser. You should use the Z offset field to adjust the focus offset so your fluorescence is in focus.

Creating a User Login

When you have a User Login all your data will automatically be saved in your own designated folder, which can be useful when trying to differentiate your data from other users' data.

1. Click the User login button in the top left of the user interface.
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2. In the dialogue box that appears, type a Username and Password and click Create user.
3. Whenever you use the machine in future, simply click User login, type in your username and password, and click Login. Your images will be saved in a folder with the same name as your username in this location: C:\Data\username.

Single colour dSTORM

Setting the acquisition conditions

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1. Click View in the Acquisition Control area to get a live feed from the acquisition camera.
   
2. There will be two live images, which correspond to two simultaneous colour channels. For dSTORM using a far-red dye you only need Channel 1, so untick Channel 0 in the Image Display Options on the left. For dyes other than far-red you will need Channel 0.
   
3. The live camera image will only show noise until you illuminate the sample with a laser. Change the percentage power in the Light Control area by either clicking on the spin buttons or typing in a value and pressing the Return key. The laser power in the image below is set to 100% but it is best to use a lower power like 10% to avoid photobleaching while setting up your specimen. Click on the button above the laser (e.g. red 640 button) to switch on the illumination.
   
4. Focus on your specimen. If you are using Z lock you may need to adjust the Z offset as explained in the section on focusing.
5. Turn off the laser when not imaging so you don’t photobleach the specimen.

Acquiring images

You can acquire data by setting conditions in the Acquisition Control area. Here you can define the exposure and number of images to be captured.

1. The best way start acquiring data is to use multidimensional acquisition. Click the Multiple Acquisition Setup button under the focus camera view on the left. In the Acquisition tab, click Single, set imaging mode to Normal, specify the laser power, exposure/frequency and number of images. In Saving, specify the Dataset Tag, which will be the folder where the files are stored, and the Acquisition Tag, which will be the filename. Note that the date will be automatically included in the filename.

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