# Overlay Manager

![Overlay Manager](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-M54VFbrPjJ1jCIDc3ve%2F-M54VO5gkUeaa4Fktu_j%2Foverlay%20manager.png?alt=media\&token=a0e3c9b6-b32e-47c5-947a-ab14f932323c)

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](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-LY_wk5Ssp2TpcTNYV_d%2F-LY_zdMnYhaoIk9vUHsp%2FoverlayManagerCheckbox.png?alt=media\&token=51d1bb1b-13c6-4d2a-843e-1786bd6abb71)

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

![Change overlay opacity](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-LY_wk5Ssp2TpcTNYV_d%2F-LYa-PyUZdbW_SkuZia2%2FoverlayManagerSlider.PNG?alt=media\&token=e15f6b11-b63e-4acc-b684-64678e838a8a)

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

![Change overlays order](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-LY_wk5Ssp2TpcTNYV_d%2F-LYa-tacGkJzJ5G6gs2l%2FoverlayManagerOrder.png?alt=media\&token=f5b0f09c-5a13-4dff-a906-96c1641f0ad4)

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](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-LpYEIh7LnRzgVv4Izum%2F-LpYMUAbjcZ16T7-GTjh%2FscaleBar.PNG?alt=media\&token=262d4c83-dc1b-42a7-a462-da43ccf79ae1)

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

#### Tile mask overlay

![Tile mask overlay](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-LlbLd5ZpgySWUvVSxO3%2F-LlbVrZM5YH2ERLGLxfO%2FtileMask.png?alt=media\&token=388ba371-6bad-4ec3-aafc-f86c096af745)

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

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

#### Segmentation overlay

![Segmentation overlay](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-LY_wk5Ssp2TpcTNYV_d%2F-LY_zDsPPzboeZ3q-mpw%2FsegmentationOverlay.PNG?alt=media\&token=03d3f573-2dc6-4e9b-8bee-c01fbd6b0df5)

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

#### Population overlay

![Population overlay](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-LY_wk5Ssp2TpcTNYV_d%2F-LY_z9_FknG99xXAbPN4%2FpopulationOverlay.PNG?alt=media\&token=455300e1-e5b8-4161-9b4f-e3b056215a4c)

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](https://help.codex.bio/codex/mav/user-instructions/population-table) for more information.

#### Voronoi overlay

![Voronoi overlay](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-LY_wk5Ssp2TpcTNYV_d%2F-LY_xxUwcyY5GlGUS5pg%2FvoronoiOverlay.png?alt=media\&token=93dfe822-471c-4772-addd-7af8dee9084f)

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

**Removed areas overlay**

![Removed areas overlay](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-LpYEIh7LnRzgVv4Izum%2F-LpYMxBkzEjCJ3sq1m2M%2FremovedAreas.PNG?alt=media\&token=fa47781d-0981-48ba-9929-510f8a96a133)

This layer shows all areas that were[ removed](https://help.codex.bio/codex/mav/region-image#remove-area) from the experiment.

#### Heatmap

![Density heatmap overlay](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-LzLmK3fqhX93yqj8uVL%2F-LzLsxQBBj9Iy-K2uy-f%2FdensityHeatmap.PNG?alt=media\&token=b63e4847-ed6d-4fd6-9c1b-c68971ef0f0e)

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