Step 2: Adjust Image Display

Step 2: Adjust Image Display#

Once data is loaded, you can fine-tune the image display using the controls in the left panel.

Channel Visibility and Colors#

Each loaded channel appears in the Channel Control Panel:

  • Visibility Toggle: Click the checkbox next to a channel name to show/hide it

  • Rename Channel: Click on the channel name to rename it

  • Change Color: Click on the color swatch to open a color picker

  • Remove Channel: Click the × button to remove a channel

See the channel control panel in the screenshot from Step 1 showing channels with checkboxes for visibility, color swatches, and remove buttons.

Per-Channel Saturation Control#

CellPick provides fine-grained saturation control for each channel:

  • Auto-adjust Saturation: When enabled (default), saturation is automatically set based on image percentiles (1st-99th)

  • Manual Saturation: Disable auto-adjust to reveal per-channel range sliders - Each slider has two handles: minimum (left) and maximum (right) - Drag handles to adjust the display range for each channel independently - The slider color matches the channel color for easy identification

See the saturation sliders below the “Auto-adjust saturation” checkbox in the screenshot from Step 1, showing per-channel range controls.

Shape Outline Color#

  • Click “Select Shape Color” to choose the outline color for displayed shapes

  • This affects how shapes are rendered on top of the image

Other View Controls#

  • Refresh: Force a redraw of the current view

  • Reset View: Reset zoom and pan to show the entire image

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