smtools 0.2.1

Redding Lab analysis tools

=======
smtools
=======

Single Molecule analysis Tools
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

.. _Redding Lab: https://www.reddinglab.com

Dependencies
------------
* numpy
* scipy
* scikit-image
* matplotlib

.. _numpy: http://www.numpy.org/
.. _scipy: https://www.scipy.org/
.. _scikit-image: https://scikit-image.org/
.. _matplotlib: https://matplotlib.org/

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.

.. code-block:: python

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()

.. figure:: https://github.com/ReddingLab/smtools/blob/master/images/alignment.png
:alt:

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

.. code-block:: python

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()

.. figure:: https://github.com/ReddingLab/smtools/blob/master/images/curtain_finder.png
:alt:


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/