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Layer Management

Each ROI in Montaris-X lives on its own layer. The Layer Panel (left sidebar) gives you full control over your ROIs.

Adding & Removing ROIs​

  • Add ROI: Click the + button. A new layer is created with a unique auto-generated name and a color from the 20-color palette.
  • Delete ROI: Select the layer and press Delete, or right-click → Delete. A confirmation dialog prevents accidental deletion.
  • Clear All: Remove all ROI layers at once from the menu.

Colors​

Montaris-X provides 20 distinct colors designed for maximum contrast on scientific images. Colors are auto-assigned but can be changed:

  • Click the color swatch next to a layer name to open the Color Palette Dialog
  • Choose from the 20 preset colors or pick a custom color
  • Colors are consistent across export formats

Naming​

  • Layers get unique auto-generated names (e.g., ROI-1, ROI-2)
  • Inline rename: Double-click a layer name to edit it directly in the panel
  • Names are preserved in .npz saves and ImageJ .roi exports

Fill Modes​

Each ROI can be displayed in one of three fill modes (set in the Properties Panel):

ModeDisplay
SolidFilled region with the layer's color
OutlineOnly the boundary edge is drawn
BothFilled region with a highlighted border

Opacity​

  • Per-layer opacity: Adjust individual layer transparency
  • Global opacity slider: In the toolbar, adjust the overlay transparency for all ROIs at once

Multi-Selection​

  • Ctrl+Click layers to add/remove them from the selection
  • Ctrl+A selects all ROIs
  • Selected ROIs can be moved, transformed, or deleted together
  • The selection syncs bidirectionally with the canvas — clicking an ROI on the canvas selects its layer, and vice versa

ROI Navigation Bar​

At the top of the Layer Panel, the Nav Bar provides quick navigation:

  • Arrow buttons to jump between ROIs
  • Shows the current ROI index and total count
  • Useful when working with many layers

Pixel Counts​

Each layer shows its pixel count — the number of non-zero pixels in the mask. This updates automatically as you draw and is useful for measuring ROI area.