bebi103.image.imshow

bebi103.image.imshow(im, cmap=None, length_units='pixels', interpixel_distance=1.0, colorbar=False, no_ticks=False, flip=True, return_im=False, saturate_channels=True, min_intensity=None, max_intensity=None, display_clicks=False, record_clicks=False, **kwargs)

Display an image in a Bokeh figure.

Parameters

  • im (Numpy array) – If 2D, intensity image to be displayed. If 3D, first two dimensions are pixel values. Last dimension can be of length 1, 2, or 3, which specify colors.

  • cmap (str or list of hex colors, default None) – If im is an intensity image, cmap is a mapping of intensity to color. If None, default is 256-level Viridis. If im is a color image, then cmap can either be ‘rgb’ or ‘cmy’ (default), for RGB or CMY merge of channels.

  • length_units (str, default 'pixels') – The units of length in the image.

  • interpixel_distance (float, default 1.0) – Interpixel distance in units of length_units.

  • colorbar (bool, default False) – If True, include a colorbar.

  • no_ticks (bool, default False) – If True, no ticks are displayed. See note below.

  • flip (bool, default True) – If True, flip image so it displays right-side up. This is necessary because traditionally images have their 0,0 pixel index in the top left corner, and not the bottom left corner.

  • return_im (bool, default False) – If True, return the GlyphRenderer instance of the image being displayed.

  • saturate_channels (bool, default True) – If True, each of the channels have their displayed pixel values extended to range from 0 to 255 to show the full dynamic range.

  • min_intensity (int or float, default None) – Minimum possible intensity of a pixel in the image. If None, the image is scaled based on the dynamic range in the image.

  • max_intensity (int or float, default None) – Maximum possible intensity of a pixel in the image. If None, the image is scaled based on the dynamic range in the image.

  • display_clicks (bool, default False) – If True, display clicks to the right of the plot using JavaScript. The clicks are not recorded nor stored, just printed. If you want to store the clicks, use the record_clicks() or draw_rois() functions.

  • record_clicks (bool, default False) – Deprecated. Use display_clicks.

  • kwargs (dict) – All other kwargs passed to bokeh.plotting.figure().

Returns

  • p (bokeh.plotting.figure instance) – Bokeh plot with image displayed.

  • im (bokeh.models.renderers.GlyphRenderer instance (optional)) – The GlyphRenderer instance of the image being displayed. This is only returned if return_im is True.