Differences

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--- usage:overlays [2019/08/06 17:00] – [Setting up the overlays] pseudomoaner
+++ usage:overlays [2022/09/05 23:04] (current) – pseudomoaner
@@ Line 31: / Line 31: @@
   * **Data colourmap:** Once you have chosen a data field to display, this menu allows you to specify the colourmap that should be used to assign colours to each element of the overlay.
-In addition to these menus, two checkboxes are available at the bottom of the settings panel: **Show ID?** and **Mark events?**. With **Show ID** selected, a small label will appear next to each object containing its track ID. **Mark events?** allows you to display externally defined events. For further details on how to assign events, please see the [[usage:advanced_usage#population_and_event_labelling|advanced usage]] section.
+In addition to these menus, two checkboxes are available at the bottom of the settings panel: **Show ID?** and **Mark events?**. With **Show ID** selected, a small label will appear next to each object containing its track ID. **Mark events?** allows you to display externally defined events. For further details on how to assign events, please see the [[usage:advanced_usage#population_and_event_labelling|advanced usage]] page.
 ===== Converting from frames to a movie =====
-Once you have triggered the bulk output, you will be able to access the set of generated frames in the new 'Overlays' folder in the root directory. You can now generate movies from these frames. There are many ways to do this, but two example methods are described below.
+Once you are happy with the setup of the overlay, click **Run 'em all!** to apply these settings to all the frames in the dataset. When this has finished, you will be able to access the set of generated frames in the new 'Overlays' folder in the root directory. You can now generate movies from these frames. There are many ways to do this, but two example methods are described below.
 ==== Method 1: Using ImageJ/FIJI ====
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 //
-==== Event detection ====
 ==== Lineage tracking ====
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 //
-The 'generational age' of each cell in this dataset is also automatically calculated in the division detection module. Cells that die stop ageing, allowing them to be clearly seen in this movie. Cell ages are indicated with a coloured mask, starting from generation 1 (dark blue) and finishing at generation 6 (dark red).
+The 'generational age' of each cell in this dataset is also automatically calculated in the division detection module. In this video, generated using the special 'Lineage trees' option, cell ages are indicated by the colour of the overlying track, starting from generation 1 (dark blue) and finishing at generation 6 (dark red).
 //
-{{ youtube>rSnvglvt-rE?large }}
+{{ youtube>AhCPggI5zz4?large }}
+//
+===== Video demonstration =====
+{{ youtube>i3EOyxx05ss?large }}