Analysis: Viewing Options

Analysis: Viewing Options

Viewing Options allows selecting the channels and localizations of interest and customizing them for rendering and visualization:

  1. Color: set the rendering parameters for visualization of both the raw images and localizations:
    1. Raw Rendering (Per Channel): customize the Color, Brightness, and Contrast for the raw rendering of each channel:
    2. Localization Rendering (Per Channel): customize the color map (Channel, Frame Index, or Z-Position), Color, thresholds (Minimum and Maximum), and localization size (Gaussian Width) for the localization rendering of each channel.
    3. Raw Rendering (Global): check to Show Maximum Projection instead of an individual frame.
    4. Localization Rendering (Global): check to Show Filtered Points In Grey instead of simply removing them or set the rendering method for localization to either Fixed or Precision, in which the rendering size of localization is defined by Gaussian Width or its exact precision value.
    5. Tracks Rendering: customize the color map (Channel, Diffusion Co., First Frame Index, or Track Length) for the track rendering.
    6. Custom Image: select an image for background rendering.
  2. Name: show the channel (raw image) index.
  3. Raw: tick to render the raw image of a channel. You can click on Raw to check/uncheck for all channels.
  4. Localizations: tick to render the localization of a channel. You can click on Localizations to check/uncheck for all channels. Note that the localization channels are linked by groups.
  5. Contrast: apply auto-contrast to a channel (raw image) once. You can click on Contrast to apply to all channels.
  6. Frame Index: select the frame to render the channel (raw image).
It is recommended to use CODI for data visualization and analysis. If at any point you are having issues with visualization, please do not hesitate to contact the CX team.


    • Related Articles

    • NimOS Analysis

      NimOS provides functions for data analysis: Analysis: Tools Analysis: Viewing Options Analysis: Filter Analysis: Localizations Analysis: Drift Correction

    • Analysis: Filter

      Results Filtering allows to set the filters for each localization channel (e.g. G0 - Left) for visualization or export, therefore suitable for PALM/dSTORM/Tracking but not for Confocal/Widefield: Disable All Filters: enable/disable all the filters ...

    • Analysis: Localizations

      In Analyze, you can override some of the default parameters used for localization. For example, changing the sigma offers the possibility to localize a bigger object, such as versicles instead of molecules. To re-run the localization, you will need ...

    • Analysis: Tools

      The Tools module allows applying different advanced tools to analyze your data: Trace: show a time series of parameters for spots found in a circular area selected from the localization data (not applicable to the raw images). To draw a circular area ...

    • Analysis: Drift Correction

      A dSTORM acquisition is usually long and subject to drift (the image being slowly shifted to one direction) caused by, for example, temperature fluctuation. Drift Correction allows correcting for the drift as post-processing. There are two methods to ...