Visualization

Source and Pre-Processed Images

Hyperstack

Source and pre-processed images can be visualized by right-clicking on the position :

If Open Input Images is selected, the source images will be displayed as a virtual hyperstack.

• Virtual means that displayed planes are loaded when needed.
• Hyperstack means that planes are displayed as a multi-dimensional stack (Z, Time, Channels)
• Channels are displayed in the order defined in the configuration

If Open Pre-Processed Images is selected, the pre-processed images will be displayed, the same way as source images.

• If there are pre-processing transformations defined for the selected position and that pre-processing has not beed performed, the command will be disabled.
• If there are no pre-processing transformations defined for the selected position, source images will be displayed.

Image 5D (Color overlay)

Instead of displaying images as a classical hyperstack, they can be displayed using the Image5D plugin. This allows to display a composite image in which each channel is associated to a color To do so:

• Define the color for each channels in the Configuration tab, parameter: Detection Channel > <Channel> > Color
• Choose the menu command Misc > Default Hyperstack Type > Image5D
• Open images the same way as normal hyperstacks

Note that Image 5D stacks are not virtual thus take more time to load.

Interactive Images

• Interactive images are images on which segmented objects and tracks can be displayed as ROI (region-of-interest) in an interactive way.
• It is highly recommended to use shortcuts.
  • Note that in this document, shortcuts are given for the AZERTY preset.
  • Preset can be selected in the menu Help > Shortcut Preset.
  • A shortcut table can be displayed from the menu command Help > Display Shortcut Table.

Open Hyperstacks

In the Segmentation & Tracking Results panel of the Data Browsing tab: Right-click on a position and choose Open Hyperstack and select the object class.

This will display an image in which the channel associated to each object class is displayed. By default, the selected object class is displayed.

Note that:

• If the Image 5D mode is activated, interactive hyperstacks are displayed with the Image5D plugin.
• You can also display hyperstack of subsets of the image: unfold a position and right-click on a item (e.g. a Nucleus) and choose Open Hyperstack : this will display the same hyperstack within the bounds of the selected object.

Open Kymographs

In BACMMAN Kymographs are images in which frames are displayed next to each other. This is the natural way of displaying mother machine data (which can be seen as 1D data). To display kymograph, choose the command Open Kymograph instead of Open Hyperstack

Display Objects and tracks

Display Interactive object class

• To display all objects, select the interactive image you which to display objects on and use the shortcut crtl + A.
• To display one or a subset of objects, select the rectangle (or freehand line) tool and click on the objects.
• To display all tracks, select the interactive image you which to display objects on and use the shortcut crtl + Q.
• To display a subset of tracks: press S to switch to track mode, select the rectangle (or freehand line) tool and click on the objects.
• If one object is selected, its attributes (index, parent, next linked object etc...) and associated measurements are displayed on right-click.

Display Selections

Selections are subsets of an object class in a given dataset. See this page for more details on selections.

To display a selection on an interactive images, right click on the selection and choose Display Objects The displayed selection will not be interactive itself (they will not disappear when clicking on the image for instance).