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1. If necessary, boot up the laptop computer and login to the ONI account.
2. Double-click the NimOS icon on the desktop to launch the acquisition and analysis software.
   
3. Click the Acquire button in the top left and then click Connect to Microscope.
   
4. NimOS will open the dialogue box below asking you to check the stage before it connects to the device to prevent damage.
   
5. Push the safety interlock slider to the in position and lift the lid of the chamber to make sure the area around the stage is clear and that all samples have been removed. There should be two stacks of small disc magnets, one stack of three on either side of the stage. They are there to secure the specimen and should be left in place.
   
6. Leave the lid open and click Confirm and Connect on the computer screen. There will be noise as the Light Engine starts up and messages will appear in NimOS as the computer connects to the different components.
7. You will see that the stage moves to very high position as part of its start-up. This is why the stage needs to be clear prior to initialisation.
8. In the Temperature Control area on the left of the user interface, set the Target Temperature to 31ºC or 37ºC and press the Enable Control button (the button with will change colour and say Disable Control once pressed). The Nanoimager operates at a temperature around 6 degrees warmer than ambient and the temperature control must be set slightly above that to maintain stability. This is something to take into consideration when planning applications where temperature is important.
   

9. Once the temperature has stabilised the control can be disabled.

   Note
   ONI say that it will take the microscope 60 to 90 minutes for the microscope to reach 37°C and stabilise.

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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 in the top left of the NimOS user interface. The focus camera view will just display a live repeating noise pattern until the focus laser is switched on.
   

   Info
   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. Type -300 µm into the Z field and gradually increase the value using the spinner (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 (see 'in focus' image below).
   

   Info
   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.
   

   Note
   The fluorescence from your specimen will most likely be at a different height to the reflections of the focus laser. The Z offset field can be used to adjust the height so sample fluorescence is in focus. See section on 'Setting acquisition conditions'.

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Setting acquisition conditions (for single colour 2D dSTORM)

The settings in the following instructions guide are appropriate for single colour 2D dSTORM using for single-channel 2D dSTORM of a sample labelled with a far - red dye like Alexa 647. Your sample or procedure may require other settings, such as an additional imaging channel, different laser wavelengths and powers, or 3D acquisition. If you need to use different settings, then you can either look for more information on the wiki or in ONI's knowledgebase (login required) or contact the light microscopy email: lmcb-lm-help@ucl.ac.uk.

1. Click the View button in the Acquisition Control area to begin 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 you can untick Channel 0 in the Image Display Options on the left. For dyes emitting wavelengths lower shorter than far-red you will need Channel 0 to be ticked (but possibly not Channel 1 if you are not using a far red dye).
   
3. The live camera image will only show noise until you illuminate the sample with a laser. Change the percentage laser power in the Light Control area by either clicking on the spinner or typing in a value and pressing the Return key. The 640 nm laser power in the image below is set to 100% for dSTORM acquisition, 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. in this case the red 640 button) to switch on the illumination.
   
4. Unless Z Lock is active you should focus on your specimen by changing the value in the Z: field (see area outlined in red in the Position Control image below). If Z lock is active the Z: position cannot be changed, so you should adjust the Z offset as explained in the section on focusing. Both the Z field and Z offset are highlighted with a red outline in the Position Control image below.
   
5. Once you're in focus turn off the laser so you don’t photobleach the specimen.

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Creating a User Login

When you have create a User Login all your data will automatically be saved in your own folder, which can be useful when trying to differentiate your data from other users' data. If you don't login, all your files will be saved in the DEFAULT_USER folder.

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Multiple Acquisition Setup

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