Contents

microfilm package

microfilm package

Submodules

microfilm.colorify module

microfilm.colorify.check_input(images, is_volume=False)

Converts input, either 2D (3D if is_volume) array, list of 2D (3D) arrays or 3D (4D) array of size DxNxM (DxZxNxM) where D<4 to list of 2D (3D) arrays.

microfilm.colorify.check_rescale_type(rescale_type, limits)

Adjust rescale_type depending on its own value and that of limits

microfilm.colorify.cmaps_def(cmap_name, num_colors=256, flip_map=False)

Return a colormap defined by its name

Parameters

  • cmap_name (str) – {‘pure_red’, ‘pure_green’, ‘pure_blue’, ‘pure_magenta’, ‘pure_cyan’, ‘pure_yellow’} or Matplotlib colormap

  • num_colors (int) – number of steps in color scale

  • flip_map (bool) – invert colormap

Returns

cmap

Return type

Matplotlib colormap

microfilm.colorify.color_translate(cmap_name)
microfilm.colorify.colorify_by_cmap(image, cmap, rescale_type='min_max', limits=None)

Directly use an existing colormap cmap to colorize an image

Parameters

  • image (2d array) – image to convert to RGB

  • cmap (Matplotlib cmap) – colormap to use for coloring

  • rescale_type (str) – ‘min_max’: between extrema values of image ‘dtype’: full range of image dtype ‘zero_max’: between zero and image max ‘limits’: between limits given by parameter limits

  • limits (list) – [min, max] limits to use for rescaling

Returns

  • image_colored (array) – 3D RGB float array

  • min_max (tuple) – actual min and max values used for rescaling

microfilm.colorify.colorify_by_hex(image, cmap_hex='#ff6600', flip_map=False, rescale_type='min_max', limits=None, num_colors=256)

Return 2D image as 3D RGB stack colored with a hex color.

Parameters

  • image (2d array) – image to convert to RGB

  • cmap_hex (str) – hex string defining color, default ‘#ff6600’

  • flip_map (bool) – invert colormap

  • rescale_type (str) – ‘min_max’: between extrema values of image ‘dtype’: full range of image dtype ‘zero_max’: between zero and image max ‘limits’: between limits given by parameter limits

  • limits (list) – [min, max] limits to use for rescaling

  • num_colors (int) – number of steps in color scale

Returns

  • image_colored (array) – 3D RGB float array

  • cmap (Matplotlib colormap object) – Generated colormap from name

  • min_max (tuple) – actual min and max values used for rescaling

microfilm.colorify.colorify_by_name(image, cmap_name, flip_map=False, rescale_type='min_max', limits=None, num_colors=256)

Return 2D image as 3D RGB stack colored with a given colormap.

Parameters

  • image (2d array) – image to convert to RGB

  • cmap_name (str) – {‘pure_red’, ‘pure_green’, ‘pure_blue’, ‘pure_magenta’, ‘pure_cyan’, ‘pure_yellow’} or Matplotlib colormap

  • flip_map (bool) – invert colormap

  • rescale_type (str) – ‘min_max’: between extrema values of image ‘dtype’: full range of image dtype ‘zero_max’: between zero and image max ‘limits’: between limits given by parameter limits

  • limits (list) – [min, max] limits to use for rescaling

  • num_colors (int) – number of steps in color scale

Returns

  • image_colored (array) – 3D RGB float array

  • cmap (Matplotlib colormap object) – Generated colormap from name

  • min_max (tuple) – actual min and max values used for rescaling

microfilm.colorify.combine_image(images, proj_type='max', alpha=0.5)

Combine a list of 3D RGB arrays into a single RGB image. The combination is done via maximum or a sum projection or via alpha blending.

Parameters

  • images (list of arrays) – list of 3d rgb(a) arrays

  • proj_type (str) – projection type of color combination max: maximum sum: sum projection, restricted to dtype range alpha: alpha blending

  • alpha (float) – transparency in range [0,1] of overlayed image(s) for proj_type == alpha

Returns

im_combined – 3D RGB array

Return type

array

microfilm.colorify.multichannel_to_rgb(images, cmaps=None, flip_map=False, rescale_type='min_max', limits=None, num_colors=256, proj_type='max', alpha=0.5, cmap_objects=None)

Convert a list of images to a single RGB image. Options can be passed as lists, one per channel, or as single element in which case the same value is used for all channel.

Parameters

  • images (list or array) – list of 2d arrays or DxMxN array where D<4

  • cmaps (list of str / Matplotlib colormaps) – colormap as names (e.g. ‘pure_red’ as specified in cmaps_def) or directly as Matplotlib colormaps (e.g. as returned by cmaps_def)

  • flip_map (bool or list of bool) – invert colormap or not

  • rescale_type (str or list of str) – ‘min_max’: between extrema values of image ‘dtype’: full range of image dtype ‘zero_max’: between zero and image max ‘limits’: between limits given by parameter limits

  • limits (list or list of lists) – [min, max] limits to use for rescaling

  • num_colors (int) – number of steps in color scale

  • proj_type (str) – projection type of color combination max: maximum sum: sum projection, restricted to dtype range alpha: alpha blending

  • alpha (float) – transparency in range [0,1] of overlayed image for proj_type == alpha

  • cmap_objects (list) – list of Matplotlib cmaps, one per channel to use for coloring if provided, no colormaps are computed and cmap names are ignored

Returns

  • converted (2d array) – multi-channel RGB image

  • cmap_objects (list) – list of Matplotlib cmaps generated for each channel

  • image_min_max (list of tuples) – actual (min, max) values used for rescaling for each image

microfilm.colorify.project_volume(images, proj_type)

Project a list of 3D images to a list of 2D images

Parameters

  • images (list of arrays) – list of 3d arrays of shape ZxNxM

  • proj_type (str) – projection type for volume max: maximum min: minimum sum: sum mean: mean

Returns

images_proj – projected arrays

Return type

list of 2D arrays (float32)

microfilm.colorify.random_cmap(alpha=0.5, num_colors=256)

Create random colormap for segmentation

microfilm.colorify.random_grandient_cmap(num_colors=25, seed=42)

Create a colormap as the gradient of a given random color

microfilm.colorify.rescale_image(image, rescale_type='min_max', limits=None)

Rescale the image between 0-1 according to a rescaling type.

Parameters

  • image (2d array) – image to scale

  • rescale_type (str) – ‘min_max’: between extrema values of image ‘dtype’: full range of image dtype ‘zero_max’: between zero and image max ‘limits’: between limits given by parameter limits

  • limits (list) – [min, max] limits to use for rescaling

Returns

  • image_rescaled (2d array)

  • min_max (tuple) – actual min and max values used for rescaling

microfilm.microanim module

class microfilm.microanim.Microanim(data, channels=None, cmaps=None, flip_map=False, rescale_type=None, limits=None, num_colors=256, proj_type='max', alpha=0.5, volume_proj=None, channel_names=None, channel_label_show=False, channel_label_type='title', channel_label_size=0.05, scalebar_thickness=0.1, scalebar_unit_per_pix=None, scalebar_size_in_units=None, unit=None, scalebar_location='lower right', scalebar_color='white', scalebar_font_size=12, scalebar_kwargs=None, scalebar_font_properties=None, ax=None, fig_scaling=3, dpi=72, label_text=None, label_location='upper left', label_color='white', label_font_size=15, label_kwargs={}, cmap_objects=None, show_colorbar=False, show_plot=True)

Bases: microfilm.microplot.Microimage

Class implementing an animation object. This object is a subclass of of the Microimage object and takes the same options. The main difference is that it takes a time-lapse dataset as obligatory parameter, not a simple image.

add_time_stamp(unit, unit_per_frame, location='upper left', timestamp_size=15, timestamp_color='white', time_format='HH:MM:SS', time_stamp_kwargs={})

Add time-stamp to movie

Parameters

  • unit (str) – unit of time ‘mmm’ millisecond, ‘SS’ seconds, ‘MM’ minute, ‘HH’ hours

  • unit_per_frame (int) – number of units per frame e.g. 5 for 5s steps

  • location (str or list) – position of the time-stamp on the image, can be ‘upper left’, ‘upper right’, ‘lower left’, ‘lower right’ or a list with xy coordinates [xpos, ypos] where 0 < xpos, ypos < 1

  • timestamp_size (int) – size of timestamp font

  • timestamp_color (str) – color of label

  • time_format (str) – How the time stamp should be represented. The string should contain the ‘HH’ for hours, ‘MM’ for minutes, ‘SS’ for seconds and ‘mmm’ for milliseconds

  • time_stamp_kwargs (dict) – additional options for label formatting passed to Matplotlib text object

save_movie(movie_name, fps=20, quality=5, format=None)
show()

Display animation object

time_range(unit, unit_per_frame, num_step, time_format='HH:MM:SS:mmm')

Create string time-stamps with arbitrary formatting.

Parameters

  • unit (str) – unit of time ‘mmm’ millisecond, ‘SS’ seconds, ‘MM’ minute, ‘HH’ hours

  • unit_per_frame (int) – number of units per frame e.g. 5 for 5s steps

  • num_steps (int) – number of steps

  • time_format (str) – How the time stamp should be represented. The string should contain the ‘HH’ for hours, ‘MM’ for minutes, ‘SS’ for seconds and ‘mmm’ for milliseconds

update_animation(t)

Update animation to time t

update_timeslider(change=None)

Update segmentation plot

class microfilm.microanim.Microanimpanel(rows, cols, margin=0.01, figscaling=5, figsize=None, channel_label_size=0.05, label_line_space=0.2, **fig_kwargs)

Bases: object

Class implementing a multi-panel animation. All animations should have the same number of time points.

Parameters

  • rows (int) – number of rows

  • cols (int) – number of columns

  • margin (float) – fraction of figure size reserved for margins between plots

  • figscaling (float) – adjust the size of the figure without providing explicit size

  • figsize (float or list) – figure size, either square or rectangular

  • dpi (int) – dots per inches passed to plt.figure

  • channel_label_size (float) – font size for channel labels (fraction of figure)

  • label_line_space (float) – space between label lines in fraction of channel_label_size

  • fig_kwargs (parameters normally passed to plt.subplots()) –

microanims

list of Microanim objects

Type

list

time_slider

time slider

Type

ipywidget slider

output

widget to display plot

Type

ipywidget Output

fig

figure containing the panel

Type

Matplotlib figure object

ax

list of Matplotlib axis objects

Type

list

ui

animation interface

Type

ipywidgets box

max_time

number of time points

Type

int

add_channel_label(channel_label_size=None, label_line_space=None)

Add channel labels to all plots and set their size

add_element(pos, microanim, fig_update=True)

Add an animation object to a panel

Parameters

  • pos (list) – i,j position of the plot in the panel

  • microanim (Microanim object) – object to add to panel

save_movie(movie_name, fps=20, quality=5, format=None)
update_animation(t)

Update all subplots

update_timeslider(change=None)

Update segmentation plot

microfilm.microanim.save_movie(anim_object, movie_name, fps=20, quality=5, format=None)

Save a movie

Parameters

  • movie_name (str or path object) – where to save the movie

  • fps (int) – frames per second

  • quality (int) – quality of images (see imageio)

  • format (str) – format for export

microfilm.microplot module

class microfilm.microplot.Microimage(images, cmaps=None, flip_map=False, rescale_type=None, limits=None, num_colors=256, proj_type='max', alpha=0.5, volume_proj=None, channel_names=None, channel_label_show=False, channel_label_type='title', channel_label_size=0.05, scalebar_thickness=0.02, scalebar_unit_per_pix=None, scalebar_size_in_units=None, unit=None, scalebar_location='lower right', scalebar_color='white', scalebar_font_size=12, scalebar_kwargs=None, scalebar_font_properties=None, ax=None, fig_scaling=3, dpi=72, label_text=None, label_location='upper left', label_color='white', label_font_size=15, label_kwargs={}, cmap_objects=None, show_colorbar=False)

Bases: object

Class implementing the plot object. It is usually created by calling the microshow function but can also be used directly.

Parameters

  • images (list or array) – list of 2d arrays or DxMxN array D<4

  • cmaps (list of str / Matplotlib colormaps or single str) – colormap can be provided as names (e.g. ‘pure_red’ as specified in cmaps_def) or directly as Matplotlib colormaps (e.g. as returned by cmaps_def) for single channel images, you can pass a single str instead of a list

  • flip_map (bool or list of bool) – invert colormap or not

  • rescale_type (str or list of str) – ‘min_max’: between extrema values of image ‘dtype’: full range of image dtype ‘zero_max’: between zero and image max ‘limits’: between limits given by parameter limits

  • limits (list or list of lists) – [min, max] limits to use for rescaling

  • num_colors (int) – number of steps in color scale

  • proj_type (str) – projection type of color combination max: maximum sum: sum projection, restricted to dtype range

  • alpha (float) – transparency in range [0,1] of overlayed image for proj_type == alpha

  • volume_proj (str) – projection type for volume images None: no projection ‘max’: maximum projection ‘sum’: sum projection, restricted to dtype range ‘mean’: mean projection

  • channel_names (list) – list of channel names

  • channel_label_show (bool) –

  • channel_label_type (str) – ‘title’, ‘in_fig’

  • channel_label_size (float) – relative font size of channel label

  • scalebar_thickness (float) – fraction of height of scale bar

  • scalebar_unit_per_pix (float) – pixel scaling (e.g. 25um per pixel)

  • scalebar_size_in_units (float) – size of scale bar in true units

  • unit (str) – name of the scale unit

  • scalebar_location (str) – upper right, lower right etc.

  • scalebar_color (str) – color of scale bar

  • scalebar_font_size (int) – size of text, set to None for no text

  • scalebar_kwargs (dict) – additional keyword arguments for scalebar

  • scalebar_font_properties (dict) – font properties for scalebar text

  • ax (Matplotlib axis) – provide existing axis

  • fig_scaling (int) – control figure scaling

  • dpi (int) – dots per inches passed to plt.figure

  • label_text (str) – image label

  • label_location (str or list) – position of the label on the image, can be ‘upper left’, ‘upper right’, ‘lower left’, ‘lower right’ or a list with xy coordinates [xpos, ypos] where 0 < xpos, ypos < 1

  • label_color (str) – color of label

  • label_font_size (int) – size of label

  • label_kwargs (dict) – additional options for label formatting passed to Matplotlib text object

  • cmaps_object (list) – list of cmap objects for each channel if provided, cmap names are ignored

  • show_colorbar (bool) – show colorbar

add_channel_labels(channel_names=None, channel_label_size=0.05)

Add the channel names color with the corresponding colormap as figure title

Parameters

  • channel_names (list) – list of channel names, defaults to channel-1, channel-2 etc.

  • channel_label_size (float) – relative font size of label

add_colorbar()

Add colorbar

add_label(label_text, label_name='default', label_location='upper left', label_color='white', label_font_size=15, label_kwargs={})

Add a figure label to an image.

Parameters

  • label_text (str) – image label

  • label_location (str or list) – position of the label on the image, can be ‘upper left’, ‘upper right’, ‘lower left’, ‘lower right’ or a list with xy coordinates [xpos, ypos] where 0 < xpos, ypos < 1

  • label_color (str) – color of label

  • label_font_size (int) – size of label

  • label_kwargs (dict) – additional options for label formatting passed to Matplotlib text object

add_scalebar(unit, scalebar_size_in_units, scalebar_unit_per_pix, scalebar_thickness=0.02, scalebar_location='lower right', scalebar_color='white', scalebar_font_size=12, scalebar_kwargs=None, scalebar_font_properties=None)

Add scalebar to an image.

Parameters

  • unit (str) – name of the scale unit

  • scalebar_size_in_units (float) – size of scale bar in true units

  • scalebar_unit_per_pix (float) – pixel scaling (e.g. 25um per pixel)

  • scalebar_thickness (float) – fraction of height of scale bar

  • scale_location (str) – upper right, lower left etc.

  • scalebar_color (str) – color of scale bar

  • scalebar_font_size (float) – relative size of text, set to None for no text

  • scalebar_kwargs (dict) – additional options for scalebar formatting passed

  • scalebar_font_properties (dict) – font properties for scalebar text

savefig(*args, **kwargs)

Save the current figure.

Call signature:

savefig(fname, *, dpi='figure', format=None, metadata=None,
        bbox_inches=None, pad_inches=0.1,
        facecolor='auto', edgecolor='auto',
        backend=None, **kwargs
       )

The available output formats depend on the backend being used.

Parameters

  • fname (str or path-like or binary file-like) –

    A path, or a Python file-like object, or possibly some backend-dependent object such as matplotlib.backends.backend_pdf.PdfPages.

    If format is set, it determines the output format, and the file is saved as fname. Note that fname is used verbatim, and there is no attempt to make the extension, if any, of fname match format, and no extension is appended.

    If format is not set, then the format is inferred from the extension of fname, if there is one. If format is not set and fname has no extension, then the file is saved with :rc:`savefig.format` and the appropriate extension is appended to fname.

  • dpi (float or ‘figure’, default: :rc:`savefig.dpi`) – The resolution in dots per inch. If ‘figure’, use the figure’s dpi value.

  • format (str) – The file format, e.g. ‘png’, ‘pdf’, ‘svg’, … The behavior when this is unset is documented under fname.

  • metadata (dict, optional) –

    Key/value pairs to store in the image metadata. The supported keys and defaults depend on the image format and backend:

    • ’png’ with Agg backend: See the parameter metadata of ~.FigureCanvasAgg.print_png.

    • ’pdf’ with pdf backend: See the parameter metadata of ~.backend_pdf.PdfPages.

    • ’svg’ with svg backend: See the parameter metadata of ~.FigureCanvasSVG.print_svg.

    • ’eps’ and ‘ps’ with PS backend: Only ‘Creator’ is supported.

  • bbox_inches (str or .Bbox, default: :rc:`savefig.bbox`) – Bounding box in inches: only the given portion of the figure is saved. If ‘tight’, try to figure out the tight bbox of the figure.

  • pad_inches (float, default: :rc:`savefig.pad_inches`) – Amount of padding around the figure when bbox_inches is ‘tight’.

  • facecolor (color or ‘auto’, default: :rc:`savefig.facecolor`) – The facecolor of the figure. If ‘auto’, use the current figure facecolor.

  • edgecolor (color or ‘auto’, default: :rc:`savefig.edgecolor`) – The edgecolor of the figure. If ‘auto’, use the current figure edgecolor.

  • backend (str, optional) – Use a non-default backend to render the file, e.g. to render a png file with the “cairo” backend rather than the default “agg”, or a pdf file with the “pgf” backend rather than the default “pdf”. Note that the default backend is normally sufficient. See the-builtin-backends for a list of valid backends for each file format. Custom backends can be referenced as “module://…”.

  • orientation ({'landscape', 'portrait'}) – Currently only supported by the postscript backend.

  • papertype (str) – One of ‘letter’, ‘legal’, ‘executive’, ‘ledger’, ‘a0’ through ‘a10’, ‘b0’ through ‘b10’. Only supported for postscript output.

  • transparent (bool) –

    If True, the Axes patches will all be transparent; the Figure patch will also be transparent unless facecolor and/or edgecolor are specified via kwargs.

    If False has no effect and the color of the Axes and Figure patches are unchanged (unless the Figure patch is specified via the facecolor and/or edgecolor keyword arguments in which case those colors are used).

    The transparency of these patches will be restored to their original values upon exit of this function.

    This is useful, for example, for displaying a plot on top of a colored background on a web page.

  • bbox_extra_artists (list of ~matplotlib.artist.Artist, optional) – A list of extra artists that will be considered when the tight bbox is calculated.

  • pil_kwargs (dict, optional) – Additional keyword arguments that are passed to PIL.Image.Image.save when saving the figure.

update(ax=None, copy=False)

Update the Microimage axis or create a new copy of the object with a new axis and figure.

Parameters

  • ax (Matplotlib axis) – Matplotlib axis to use for plot

  • copy (bool) – create a new figure for plot, by default False

Returns

microim – object is returned

Return type

if a new plot object is created (copy==True), the

class microfilm.microplot.Micropanel(rows, cols, margin=0.01, figscaling=5, figsize=None, channel_label_size=0.05, label_line_space=0.2, **fig_kwargs)

Bases: object

Class implementing a panel object of multiple Microimage objects.

Parameters

  • rows (int) – number of panel rows

  • cols (int) – number of panel columns

  • margin (float) – fraction of figure size reserved for margins between plots

  • figscaling (float) – adjust the size of the figure without providing explicit size

  • figsize (list) – figure size [x, y]

  • channel_label_size (float) – font size for channel labels (fraction of figure)

  • fig_kwargs (parameters normally passed to plt.subplots()) –

fig
Type

Matplotlib figure object

ax

list of Matplotlib axis objects

Type

list

microplots

array of Microimage objects

Type

2d array

add_channel_label(channel_label_size=None, label_line_space=None)

Add channel labels to all plots and set their size

add_element(pos, microim)

Add a microimage object to a panel

Parameters

  • pos (list) – i,j position of the plot in the panel

  • microim (Microim object) – object to add to panel

construct_figure()

Construct the figure

savefig(*args, **kwargs)

Save the current figure.

Call signature:

savefig(fname, *, dpi='figure', format=None, metadata=None,
        bbox_inches=None, pad_inches=0.1,
        facecolor='auto', edgecolor='auto',
        backend=None, **kwargs
       )

The available output formats depend on the backend being used.

Parameters

  • fname (str or path-like or binary file-like) –

    A path, or a Python file-like object, or possibly some backend-dependent object such as matplotlib.backends.backend_pdf.PdfPages.

    If format is set, it determines the output format, and the file is saved as fname. Note that fname is used verbatim, and there is no attempt to make the extension, if any, of fname match format, and no extension is appended.

    If format is not set, then the format is inferred from the extension of fname, if there is one. If format is not set and fname has no extension, then the file is saved with :rc:`savefig.format` and the appropriate extension is appended to fname.

  • dpi (float or ‘figure’, default: :rc:`savefig.dpi`) – The resolution in dots per inch. If ‘figure’, use the figure’s dpi value.

  • format (str) – The file format, e.g. ‘png’, ‘pdf’, ‘svg’, … The behavior when this is unset is documented under fname.

  • metadata (dict, optional) –

    Key/value pairs to store in the image metadata. The supported keys and defaults depend on the image format and backend:

    • ’png’ with Agg backend: See the parameter metadata of ~.FigureCanvasAgg.print_png.

    • ’pdf’ with pdf backend: See the parameter metadata of ~.backend_pdf.PdfPages.

    • ’svg’ with svg backend: See the parameter metadata of ~.FigureCanvasSVG.print_svg.

    • ’eps’ and ‘ps’ with PS backend: Only ‘Creator’ is supported.

  • bbox_inches (str or .Bbox, default: :rc:`savefig.bbox`) – Bounding box in inches: only the given portion of the figure is saved. If ‘tight’, try to figure out the tight bbox of the figure.

  • pad_inches (float, default: :rc:`savefig.pad_inches`) – Amount of padding around the figure when bbox_inches is ‘tight’.

  • facecolor (color or ‘auto’, default: :rc:`savefig.facecolor`) – The facecolor of the figure. If ‘auto’, use the current figure facecolor.

  • edgecolor (color or ‘auto’, default: :rc:`savefig.edgecolor`) – The edgecolor of the figure. If ‘auto’, use the current figure edgecolor.

  • backend (str, optional) – Use a non-default backend to render the file, e.g. to render a png file with the “cairo” backend rather than the default “agg”, or a pdf file with the “pgf” backend rather than the default “pdf”. Note that the default backend is normally sufficient. See the-builtin-backends for a list of valid backends for each file format. Custom backends can be referenced as “module://…”.

  • orientation ({'landscape', 'portrait'}) – Currently only supported by the postscript backend.

  • papertype (str) – One of ‘letter’, ‘legal’, ‘executive’, ‘ledger’, ‘a0’ through ‘a10’, ‘b0’ through ‘b10’. Only supported for postscript output.

  • transparent (bool) –

    If True, the Axes patches will all be transparent; the Figure patch will also be transparent unless facecolor and/or edgecolor are specified via kwargs.

    If False has no effect and the color of the Axes and Figure patches are unchanged (unless the Figure patch is specified via the facecolor and/or edgecolor keyword arguments in which case those colors are used).

    The transparency of these patches will be restored to their original values upon exit of this function.

    This is useful, for example, for displaying a plot on top of a colored background on a web page.

  • bbox_extra_artists (list of ~matplotlib.artist.Artist, optional) – A list of extra artists that will be considered when the tight bbox is calculated.

  • pil_kwargs (dict, optional) – Additional keyword arguments that are passed to PIL.Image.Image.save when saving the figure.

microfilm.microplot.microshow(images=None, cmaps=None, flip_map=False, rescale_type=None, limits=None, num_colors=256, proj_type='max', alpha=0.5, volume_proj=None, channel_names=None, channel_label_show=False, channel_label_type='title', channel_label_size=0.05, scalebar_thickness=0.02, scalebar_unit_per_pix=None, scalebar_size_in_units=None, unit=None, scalebar_location='lower right', scalebar_color='white', scalebar_font_size=12, scalebar_kwargs=None, scalebar_font_properties=None, ax=None, fig_scaling=3, dpi=72, label_text=None, label_location='upper left', label_color='white', label_font_size=15, label_kwargs={}, cmap_objects=None, show_colorbar=False, microim=None)

Plot image

Parameters

  • images (list or array) – list of 2d arrays or DxMxN array D<4

  • cmaps (list of str / Matplotlib colormaps or single str) – colormap can be provided as names (e.g. ‘pure_red’ as specified in cmaps_def) or directly as Matplotlib colormaps (e.g. as returned by cmaps_def) for single channel images, you can pass a single str instead of a list

  • flip_map (bool or list of bool) – invert colormap or not

  • rescale_type (str or list of str) – ‘min_max’: between extrema values of image ‘dtype’: full range of image dtype ‘zero_max’: between zero and image max ‘limits’: between limits given by parameter limits

  • limits (list or list of lists) – [min, max] limits to use for rescaling

  • num_colors (int) – number of steps in color scale

  • proj_type (str) – projection type of color combination max: maximum sum: sum projection, restricted to dtype range alpha: alpa blending

  • alpha (float) – transparency in range [0,1] of overlayed image for proj_type == alpha

  • volume_proj (str) – projection type for volume images None: no projection ‘max’: maximum projection ‘sum’: sum projection, restricted to dtype range ‘mean’: mean projection

  • channel_names (list) – list of channel names

  • channel_label_show (bool) –

  • channel_label_type (str) – ‘title’, ‘in_fig’

  • channel_label_size (float) – relative font size for channel labels

  • scalebar_thickness (float) – fraction height of scale bar

  • scalebar_unit_per_pix (float) – pixel scaling (e.g. 25um per pixel)

  • scalebar_size_in_units (float) – size of scale bar in true units

  • unit (str) – name of the scale unit

  • scale_location (str) – upper right, lower left etc.

  • scalebar_color (str) – color of scale bar

  • scalebar_font_size (int) – size of text, set to None for no text

  • scalebar_kwargs (dict) – additional options for scalebar formatting passed

  • scalebar_font_properties (dict) – font properties for scalebar text

  • ax (Matplotlib axis) – provide existing axis

  • fig_scaling (int) – control figure scaling

  • dpi (int) – dots per inches passed to plt.figure

  • label_text (str) – image label

  • label_location (str or list) – position of the label on the image, can be ‘upper left’, ‘upper right’, ‘lower left’, ‘lower right’ or a list with xy coordinates [xpos, ypos] where 0 < xpos, ypos < 1

  • label_color (str) – color of label

  • label_font_size (int) – size of label

  • label_kwargs (dict) – additional options for label formatting passed to Matplotlib text object

  • cmap_objects (list) – list of Matplotlib colormaps to use for coloring if provided, the cmap names are ignored

  • show_colorbar (bool) – show colorbar

  • microim (Microimage object) – object to re-use

Return type

Microimage object

microfilm.microplot.volshow(images, volume_proj='mean', **kwargs)

Plot volume

images: list or array

list of 2d arrays or DxMxN array D<4

cmaps: list of str / Matplotlib colormaps or single str

colormap can be provided as names (e.g. ‘pure_red’ as specified in cmaps_def) or directly as Matplotlib colormaps (e.g. as returned by cmaps_def) for single channel images, you can pass a single str instead of a list

flip_map: bool or list of bool

invert colormap or not

rescale_type: str or list of str

‘min_max’: between extrema values of image ‘dtype’: full range of image dtype ‘zero_max’: between zero and image max ‘limits’: between limits given by parameter limits

limits: list or list of lists

[min, max] limits to use for rescaling

num_colors: int

number of steps in color scale

proj_type: str

projection type of color combination max: maximum sum: sum projection, restricted to dtype range alpha: alpa blending

alpha: float

transparency in range [0,1] of overlayed image for proj_type == alpha

volume_proj: str

projection type for volume images None: no projection ‘max’: maximum projection ‘sum’: sum projection, restricted to dtype range ‘mean’: mean projection

channel_names: list

list of channel names

channel_label_show: bool channel_label_type: str

‘title’, ‘in_fig’

channel_label_size: float

relative font size for channel labels

scalebar_thickness: float

fraction height of scale bar

scalebar_unit_per_pix: float

pixel scaling (e.g. 25um per pixel)

scalebar_size_in_units: float

size of scale bar in true units

unit: str

name of the scale unit

scale_location: str

upper right, lower left etc.

scalebar_color: str

color of scale bar

scalebar_font_size: int

size of text, set to None for no text

scalebar_kwargs: dict

additional options for scalebar formatting passed

scalebar_font_properties: dict

font properties for scalebar text

ax: Matplotlib axis

provide existing axis

fig_scaling: int

control figure scaling

dpi: int

dots per inches passed to plt.figure

label_text: str

image label

label_location: str or list

position of the label on the image, can be ‘upper left’, ‘upper right’, ‘lower left’, ‘lower right’ or a list with xy coordinates [xpos, ypos] where 0 < xpos, ypos < 1

label_color: str

color of label

label_font_size: int

size of label

label_kwargs: dict

additional options for label formatting passed to Matplotlib text object

cmap_objects: list

list of Matplotlib colormaps to use for coloring if provided, the cmap names are ignored

show_colorbar: bool

show colorbar

microim: Microimage object

object to re-use

Microimage object

microfilm.version module

Module contents

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microfilm.dataset package