smtools 0.2.2

Redding Lab analysis tools

This package contains tools analysis package of the Redding Lab, at the University of Cailfornia, San Francisco.

Dependencies

• numpy

• scipy

• scikit-image

• matplotlib

Installation

The easiest way to install the package is via pip:

$ pip install smtools

Documentation

Documentation: https://smtools.readthedocs.io/en/latest/

Usage

The smtools.algnment module is designed to align images split into separate channels. It relies on using fluorescent particles that appear on both channels. When executed, the following code will yield the image output below.

import smtools.testdata as test
import smtools.alignment as al
import matplotlib.pyplot as plt
dx, dy, params = al.inspect_global_fit(test.image_stack(), showplot=False)
im = test.image_stack()[0]
im_old = al.overlay(im)
im_adj_image = al.align_by_offset(im,dx,dy)
im_new = al.overlay(im_adj_image)
fig = plt.figure(figsize=(12,12))
ax1 = fig.add_subplot(211)
ax2 = fig.add_subplot(212,sharex=ax1)
ax1.set_title('Original Image', fontsize = "18")
ax2.set_title('Aligned Image', fontsize = "18")
ax1.imshow(im_old)
ax2.imshow(im_new)
plt.show()

The smtools.curtains module is designed to locate individual DNA molecules within a DNA curtain.

import smtools.curtains as cs
import smtools.alignment as al
from scipy.ndimage.interpolation import rotate
import matplotlib.pyplot as plt
import smtools.testdata as test
im = test.test_curtain()
ch1,ch2 = al.im_split(im)
angle = cs.find_rotang(ch2)
rotated_ch2 = rotate(ch2,angle)
bounds, mask = cs.find_curtain(rotated_ch2)
strands = cs.find_DNA(rotated_ch2,bounds)
DNAs = cs.fit_DNA(rotated_ch2, strands)
fig = plt.figure(figsize=(5,10))
plt.axis('off')
plt.imshow(rotated_ch2)
for x0,x1,y in DNAs:
    plt.plot([x0,x1],[y,y],"r.", markersize = 5)
plt.show()

Version History

• 0.1.0 Initial release with alignment, point_fitting modules

• 0.2.0 Included curtains and misc modules

References

• PyPI Page: https://pypi.org/project/smtools/

• Readthedocs: https://smtools.readthedocs.io/en/latest/