Copy To Clipboard (Raw)

1. Right-click on any of the channels and click on Copy To Clipboard:
   
   
2. Paste it into any other data viewer (e.g. ImageJ, Paint, Excel...) to visualize and save the entire live view panel:
   
   

1. You can also copy/paste the rendering from Analyze or Focus Camera View.

Export Localization Rendering (Localization)

1. Pixel Size: set the pixel size in nm.
   
2. Color Mode: set image format to either Color (RGB) or Grayscale.
   
3. Region To Export: set the export region to either Displayed Region or Full Region, where the former renders the viewport specified in Analyze and the latter renders only the field of view.
   
4. Contrast Adjustment: set the thresholds for normalization.

1. In Analyze, load the data and adjust the viewport for export.
   
2. Click on Data > Export Localization Rendering to open the export window.
   
3. In the pop-up window, set the export options and click on Export to save the rendering to a Tiff file.

1. If Displayed Region is selected, the viewport needs to be manually adjusted to cover the entire imaging field of view.
   

Export Localization As .CSV (Localization)

1. In Setting > User Settings, check the desired export options.
2. In Analyze, load the data and apply the desired filters.
   
3. Click on Export Localizations As .CSV to save the filtered localization data to a CSV file.
   

1. The exported CSV file may not be natively compatible with 3rd party software such as ImageJ-ThunderSTORM, and an additional process is required to feed the data. For detailed instructions, check here.
   

Export Mapped Channel Crops To Tiff (Raw)

1. In Analyze, load the data.
   
2. Click on Data > Export Mapped Channel Crops To Tiff to open the export window.
   
3. Check Apply Camera Calibration to export the rendering with the camera calibration applied (exported images will be in photon counts).
   
4. In the pop-up window, select the channels to export and click on Export to save the channels to an ImageJ Hyperstack.
   
   

1. The two channels are labeled as "C" and the total number of frames is labeled as "T" in the Hyperstack:
   
   
   
2. It is known that the export is not working as expected if the channels are not having the same frame count.

Batch Processing (Raw and Localization)

1. Click on Data > Batch Processing to open the processing window.
   
2. In the pop-up window, click on Open Folder to select the folder of interest.
   
3. Click on Add to add a dataset or click on Add All Data Sets to add all the datasets in this folder for batch processing.
   
4. Check the export options and click on Start Processing to start the batch processing:
   
   
   
5. Click on Create Hyperstack to combine the raw images of the selected datasets into an ImageJ Hyperstack:
   
1. Set a file name in Datatag Of Combined Dataset.
   
2. Click on Create Hyperstack to open the export window.
   
3. In the pop-up window, set the correct export parameters and click on OK to save the Hyperstack:
   

   

   where Z Positions correspond to Z-stacking, Time points correspond to timelapse, Channels correspond to the two channels, and Colors correspond to the laser sequence.
   

1. If only Run Localization is checked, all the selected datasets will be localized and the original localization results will be overwritten.
   
2. If only Export CSV is checked, all the selected datasets will be exported as CSV files and saved in the same folder from which the dataset was added. If Channel 0 and/or Channel 1 are checked, only the localizations from the selected channels will be exported.
   
3. If only Channel 1 and/or Channel 1 are checked, the selected channels will be exported as Tiff files with the channel mapping calibration applied (but without camera calibration).
4. For more detailed instructions on how to export the localization data for ImageJ/ThunderSTORM analysis, check here.
   
5. NimOS uses the default Hypderstack format "XYZCT", in which the export may not work as expected if multiple frames are acquired per color/laser. The best way to create a Hyperstack would be to load all the frames into ImageJ and build a Hyperstack with a custom order.

 If at any point you are having issues with the export process, please do not hesitate to contact the CX team.