Colormaps¶

stackview supports colormaps as defined in Matplotlib and aims at compatibility with microfilm.

In [1]:

import stackview
import numpy as np
from skimage.io import imread

In [2]:

image = imread("data/blobs.tif")

You can show images with colormaps such as pure_green, pure_red, pure_magenta_r. The _r by the end specifies that low values correspond to high intensity.

In [3]:

stackview.slice(image, colormap="pure_magenta_r")

Out[3]:

VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=254, width=256),)),)), IntSlider(value=127, de…

In [4]:

stackview.curtain(image, image, colormap="pure_green", curtain_colormap="pure_green_r")

Out[4]:

VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=254, width=256),)),)), IntSlider(value=127, de…

As imswitch() shows a list (or dictionary) of images, you can also specify a list of colormaps.

In [5]:

stackview.switch(
    [image, image, image],
    colormap=["pure_magenta", "pure_green", "pure_cyan"]
)

Out[5]:

VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=254, width=256),)),)), HBox(children=(Button(d…

You can also specify a single colormap for all images.

In [6]:

stackview.switch(
    [image, image[::-1], image[:,::-1]],
    colormap="pure_green"
)

Out[6]:

VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=254, width=256),)),)), HBox(children=(Button(d…

In [7]:

stackview.crop(image, colormap='pure_green')

Out[7]:

_Cropper(children=(IntRangeSlider(value=(0, 254), description='Y', max=254), IntRangeSlider(value=(0, 256), de…

In [8]:

labels = np.zeros_like(image, dtype=np.uint32)
labels[10:20, 10:20] = 1

stackview.annotate(image, labels, colormap="pure_magenta")

Out[8]:

VBox(children=(HBox(children=(HBox(children=(VBox(children=(ImageWidget(height=254, width=256),)),)), VBox(chi…

In [9]:

def flip(image, flip_x:bool, flip_y:bool):
    if flip_x:
        image = image[...,::-1]
    if flip_y:
        image = image[::-1]
    return image
    
stackview.interact(flip, image, colormap="pure_magenta")

Out[9]:

VBox(children=(interactive(children=(Checkbox(value=False, description='flip_x'), Checkbox(value=False, descri…

In [10]:

mri = imread("data/Haase_MRT_tfl3d1.tif")

stackview.orthogonal(mri, colormap="pure_green")

Out[10]:

HBox(children=(VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=160, width=160),)),)), IntSlide…

In [11]:

stackview.picker(mri, colormap="pure_green")

Out[11]:

VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=160, width=160),)),)), IntSlider(value=60, des…

Display range¶

One can also tune the display range by providing the minimum and maximum intensity that should be shown.

In [12]:

stackview.slice(image, display_max=100)

Out[12]:

VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=254, width=256),)),)), IntSlider(value=127, de…

In [13]:

stackview.slice(image, display_min=50)

Out[13]:

VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=254, width=256),)),)), IntSlider(value=127, de…

Muliti-channel images¶

To overlay multi-channel images with defined colormaps per channel, you can also stackview.switch() with toggleable=True.

In [14]:

hela_cells = imread("data/hela-cells.tif")

stackview.switch(
    {"lysosomes":   hela_cells[:,:,0],
     "mitochondria":hela_cells[:,:,1],
     "nuclei":      hela_cells[:,:,2]
    },
    colormap=["pure_magenta", "pure_green", "pure_blue"],
    toggleable=True
)

Out[14]:

VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=512, width=672),)),)), HBox(children=(ToggleBu…