How to guide: Visualization panel

How to guide: Visualization panel

Tool view

Note: the visualisation panel is visible in all current CODI widgets on the left hand side of the screen.


Purpose of tool

Enables the user to customise the main view of the dSTORM acquisition.


  • 2D options

  • 3D options

  • Channel options

2D options


  • Brightness: The first slider in the visualisation widget controls the brightness of each channel in the image.

    • When the toggle is set to perc. (percentile) the value of the slider refers to a threshold on the intensity distribution of the pixels in the current view on CODI. Every pixel that has an intensity value higher than this threshold will be saturated to the maximum intensity value of the screen. For example, if the threshold is 90, then the pixels in the top 10% of the intensities in the current view will be saturated to the maximum pixel intensity. If the threshold is lowered then more pixels in the view are saturated and therefore the image appears brighter.

    • When the toggle is set to raw, the intensity values of the localisations are set to the maximum pixel value that the screen can display divided by the value selected on the slider. Therefore setting the raw threshold lower will increase the brightness of the image. For example if the value is set to 2, all of the localisations in the view will have the intensity of the maximum pixel divided by 2.

  • Localisation viewing: The second slider determines how the localisations are viewed.

    • When the toggle is set to fixed, the slider determines the standard deviation of the Gaussian used to render that localisation.

    • When the toggle is set to precis. (precision), the standard deviation of the Gaussian is set to the precision of the localisation.

  • Reset camera: Resets the view to the default view when a dataset is loaded.

3D options


  • The Z exaggeration slider will stretch the data in the z-direction by multiplying the z coordinate of each localisation by the value on the slider. For instance, if the value is set to 10, then the z values will be multiplied by 10. It can be used to enhance the depth of an image as the depth in z is much smaller than the dimensions of the xy plane

  • The toggle for z-scale will make the 3D grid lines appear

  • The toggle between the orth (orthographic) and persp (perspective) view allows the user to select the corresponding projection in 3D.

Channel options

  • The eye symbol next to each channel allows the user to show or hide channels in the visualisation

  • Each channel can be selected by clicking on its name, it will highlight in a colour matching its color map. To interact with the data in a given channel, it has to be selected from this panel. For example to filter specific channels in the filtering tool you can select them like this.

  • The user can click on the color map to select a coloring scheme for data in that channel

  • The property selection dropdown, which shows locs (localisations) by default, defines the property of the localisations being use to define the colour. If ‘locs’ is selected then each localisation will have the colour defined for that channel. The user can choose different features they would like to color by.

  • For color maps with gradients a slider will appear in the channel menu. This slider can be used to adjust the subset of the color map a user wants to visualise

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