The Pixel tool (shortcut X, Shift-B if the Pencil tool is selected) draws pixel components. Use the pixel tool to create pixel fonts and pixel symbols.
The Pixel tool requires a grid spacing of 2 or above. Change it in File → Font Info… → Other → Grid Spacing. See Grid Spacing & Subdivision for details.
The Pixel tool uses the glyph named pixel to draw pixels when clicking and dragging in Edit View. If the glyph named pixel is not already in the font, Glyphs will offer to add it upon a click with the Pixel tool:
Click Add to create the pixel glyph. By default, the pixel glyph is a square of the same size as the grid spacing.
Select the Pixel tool, click once, and add a pixel component on the canvas. Click again to remove the pixel. Click and drag the mouse to add multiple pixels. Start to drag on a pixel already in place to remove pixels while dragging.
The pixel glyph can be modified to contain any arbitrary shape. Reduce the grid spacing to a lower number (for example, the default of 1) to draw path segments smaller than a pixel. For instance, the pixel can be an x-mark for a stitch effect. Increase the grid spacing again when using the Pixel tool.