How to guide: Visualization panel

How to guide: Visualization panel

For the moment CODI is only able to display super-resolution microscopy data, meaning images create from localizations of blinking event. For the visualisation or analysis of raw images, such as brightfield, widefield or tracking, please us NimOS or other software of your choice.  

To visualise your data, you first need to select an acquisition. To learn how to select acquisition please refer to the CODI overview guide. 

Tool view

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


  •  Set Camera : allows the user to choose how to position the image and mostly with which zoom. This allows the user to take screenshot of the exact same position or with the exact same scale bar (zoom) if needed, either of different acquisition, different areas or when analysing data later on. 
     Reset camera  will reset the view to the default one (centered). 

  • Brightness: The  auto  /  manual  box and the first slider on the top controls the brightness of each channel in the image.

    • When the toggle is set to  auto . (percentile) the value of the slider refers to a threshold on the intensity distribution of the pixels in the image. 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  manual , 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.

  •  Outline hidden/show : will draw a box around the acquisition. This can be useful to see the boundaries of the images in 2D and mostly in 3D. 

  • Localisation viewing: The  Fixed  /  precis.  and 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. In other words, every localisation has the same size and the slider allows the user to change that size. 

    • When the toggle is set to precis. (precision), the standard deviation of the Gaussian is set to the precision of the localisation. In other words, the size and intensity of localisation is dependant on how precisely it was localised. Small and bright are good localisation while large and dim aren't so good. 

3D options

  • The toggle between the orth (orthographic) and persp (perspective) view allows the user to select the corresponding projection in 3D.
    Orthographic will give a real 3D rendering of an objective, where parallel lines stays parallel even at an infinite distance. Perspective on the other hand will have parallel lines converging at some point. While this is less scientifically acurrate and more accurate, it can also be more pleasing to the eye, 

  • 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

Channel options

  • The Toggle button next to each channel allows the user to show or hide channels and data. 

  • Each channel can be selected by clicking on its name, it will highlight in a colour matching with the localisations. If any slider is moved, all the selected channels will be moving together. To choose specific settings for one channel, be sure to unselect and select the appropriate one. 

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

  • The property selection dropdown, which shows locs  (localisations) by default, defines the property of the localisations being use for a colouring.
    For example
    if  Frame index  is selected, the colour of a localisation will depend on which frame it was detected.
    With  Z (nm)  the colour will depend on its position in Z (if the data was taken as 3D, in 2D all the localisation will have the same colour. 
    Other available options are 
     Photon count , Sigma , P-value , localisation precision  Background  which are all filters more describe in the filter section. All those are good options to visualise specific information of the data and their homogeneity or differences. 

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

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