add README figure legend

README.md

@@ -80,7 +80,17 @@ For more detailed information on package usage and functionality, please refer t
 
 ## Application overview
 
-![**Figure 1: cytoviewer interface and functionality.** **(A)** The supported functionality (right) of *cytoviewer* depends on the data inputs (left). To match information between the objects, cell (cell_id) and image (img_id) identifiers can be provided. SCE/SPE = *SingleCellExperiment*/*SpatialExperiment*. **(B)** The graphical user interface of *cytoviewer* is divided into a body, header, and sidebar. The body of *cytoviewer* includes the image viewer, which has three tabs: Composite (Image-level), Channels (Image-level), and Mask (Cell-level). Zooming is supported for Composite and Mask tabs. The package version, R session information, help page, and a drop-down menu for image downloads are located in the header. The sidebar menu has controls for sample selection, image visualization, mask visualization, and general settings. Scale bar: 150 µm **(C)** *cytoviewer* supports different viewing modes. Top: The "channels" tab of image-level visualization displays individual channels. Shown are Ecad (magenta), CD8a (cyan), and CD68 (yellow) marking tumor cells, CD8+ T cells, and myeloid cells, respectively. Center: The "composite" tab of image-level visualization visualizes image composites combining multiple channels. These composite images can be overlayed with cell outlines, which can be colored by cell-specific metadata. Shown here are cell outlines colored by cell area (continous value) and cell type (categorical value; tumor cells in white). Channel color settings are as follows for all markers: Contrast: 2,5; Brightness: 1; Gamma: 1.2. Bottom: The "mask" tab can be used to visualize segmentation masks that can be colored by cell-specific metadata. Shown here are segmentation masks colored by cell area (continuous) and cell type (categorical; tumor cells in magenta). Scale bars: 150 µm. **(D)** "Image appearance" controls can be used to add legends or titles and to change the scale bar length for image-level (top) and cell level (bottom) visualization. The cell-level mask plot depicts tumor (magenta), myeloid (yellow), and CD8+ T cells (cyan). Scale bars: 100 µm. **Adapted from Meyer et al., 2024**](vignettes/imgs/cytoviewer_overview.png)
+![**Figure 1: cytoviewer interface and functionality.**](vignettes/imgs/cytoviewer_overview.png)
+
+**(A)** The supported functionality (right) of *cytoviewer* depends on the data inputs (left). To match information between the objects, cell (cell_id) and image (img_id) identifiers can be provided. SCE/SPE = *SingleCellExperiment*/*SpatialExperiment*.
+
+**(B)** The graphical user interface of *cytoviewer* is divided into a body, header, and sidebar. The body of *cytoviewer* includes the image viewer, which has three tabs: Composite (Image-level), Channels (Image-level), and Mask (Cell-level). Zooming is supported for Composite and Mask tabs. The package version, R session information, help page, and a drop-down menu for image downloads are located in the header. The sidebar menu has controls for sample selection, image visualization, mask visualization, and general settings. Scale bar: 150 µm
+
+**(C)** *cytoviewer* supports different viewing modes. Top: The "channels" tab of image-level visualization displays individual channels. Shown are Ecad (magenta), CD8a (cyan), and CD68 (yellow) marking tumor cells, CD8+ T cells, and myeloid cells, respectively. Center: The "composite" tab of image-level visualization visualizes image composites combining multiple channels. These composite images can be overlayed with cell outlines, which can be colored by cell-specific metadata. Shown here are cell outlines colored by cell area (continous value) and cell type (categorical value; tumor cells in white). Channel color settings are as follows for all markers: Contrast: 2,5; Brightness: 1; Gamma: 1.2. Bottom: The "mask" tab can be used to visualize segmentation masks that can be colored by cell-specific metadata. Shown here are segmentation masks colored by cell area (continuous) and cell type (categorical; tumor cells in magenta). Scale bars: 150 µm.
+
+**(D)** "Image appearance" controls can be used to add legends or titles and to change the scale bar length for image-level (top) and cell level (bottom) visualization. The cell-level mask plot depicts tumor (magenta), myeloid (yellow), and CD8+ T cells (cyan). Scale bars: 100 µm. 
+
+**Adapted from Meyer et al., 2024**
 
 ## Contributing