smtools
Single Molecule analysis Tools
This package contains a package written for the analysis of single molecule data by 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
Alignment
The smtools.algnment module is designed to align images that were split into separate channels during data collection. It relies on using fluorescent particles that appear in both channels. To see how it works see our walkthrough here . Also finding maxima and fitting gaussians.
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()
Detecting DNA curtains
The smtools.curtains module is designed to locate, and fit the intensity profile of individual DNA molecules within a DNA curtain. For a description of how it works see our walkthroughs part 1, part 2, and part 3.
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
- Github: https://github.com/ReddingLab/smtools/
- PyPI Page: https://pypi.org/project/smtools/
- Readthedocs: https://smtools.readthedocs.io/en/latest/
