> For the complete documentation index, see [llms.txt](https://help.codex.bio/codex/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.codex.bio/codex/mav/user-instructions/overlay-manager.md).

# Overlay Manager

![Overlay Manager](/files/-M54VO5gkUeaa4Fktu_j)

In this internal frame you are able to manage all overlays on region images. There are three types of overlay layers: Segmentation, Population and Voronoi. 

![Change overlay visibility](/files/-LY_zdMnYhaoIk9vUHsp)

You can change visibility of each layer by clicking on corresponding checkboxes.

![Change overlay opacity](/files/-LYa-PyUZdbW_SkuZia2)

Also you can set opacity of each layer by adjusting corresponding sliders.

![Change overlays order](/files/-LYa-tacGkJzJ5G6gs2l)

All overlays are placed in specific order. You can change order of overlays be clicking on up/down arrow buttons.

#### **Scale bar overlay**

![Scale bar overlay](/files/-LpYMUAbjcZ16T7-GTjh)

This layer shows the distance between two points on the [region image](/codex/mav/user-instructions/region-image.md)**.** 

#### Tile mask overlay

![Tile mask overlay](/files/-LlbVrZM5YH2ERLGLxfO)

This layer shows the tile numbers net on the region image. 

*Note:* In different experiments tile ordering may be different.

#### Segmentation overlay

![Segmentation overlay](/files/-LY_zDsPPzboeZ3q-mpw)

This layer shows the cell segmentation outlines from the current segmentation run. Outlines are randomly colored.

#### Population overlay

![Population overlay](/files/-LY_z9_FknG99xXAbPN4)

This layer is connected to the Population Manager and it is disabled by default. It will become enabled after at least one population is created. See [Population table](/codex/mav/user-instructions/population-table.md) for more information.

#### Voronoi overlay

![Voronoi overlay](/files/-LY_xxUwcyY5GlGUS5pg)

This layer relates with Voronoi diagram and it is disabled by default. It will become enabled after Voronoi diagram is calculated. See [Voronoi diagram](/codex/mav/user-instructions/voronoi-diagram.md) for more information.

**Removed areas overlay**

![Removed areas overlay](/files/-LpYMxBkzEjCJ3sq1m2M)

This layer shows all areas that were[ removed](/codex/mav/user-instructions/region-image.md#remove-area) from the experiment.

#### Heatmap

![Density heatmap overlay](/files/-LzLsxQBBj9Iy-K2uy-f)

This layer relates with Density heatmap and it is disabled by default. It will become enabled after Density heatmap is calculated. See [Density heatmap](/codex/mav/user-instructions/other-analysis-operations.md#density-heatmap) for more information. 


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