Multiscale modified by Lam Son

Lam Son — Sat, 21 Feb 2015 22:11:34 -0000

Multiscale modified by Lam Son

Lam Son — Sat, 21 Feb 2015 22:11:04 -0000

Multiscale modified by Lam Son

Lam Son — Sat, 21 Feb 2015 22:10:34 -0000

--- v1
+++ v2
@@ -1,3 +1,5 @@
+
+[[include repo=code path=trunc/python/colloids/notebooks/Multiscale.html]]

 # Multiscale localisation

Multiscale modified by Lam Son

Lam Son — Sat, 21 Feb 2015 22:04:32 -0000

Multiscale localisation

First, import necessary library to load and display images

import numpy as np
from matplotlib import pyplot as plt
from colloids import track
%matplotlib inline

We also need to define a function to quickly plot circles of different sizes on
a figure

def draw_circles(xs, ys, rs, **kwargs):
    for x,y,r in zip(xs,ys,rs):
        circle = plt.Circle((x,y), radius=r, **kwargs)
        plt.gca().add_patch(circle)

Load a picture containing bright particles on a dark background and immediatly
display this image in a figure

im = plt.imread('droplets.jpg')
plt.imshow(im, 'hot');
plt.show()

Create a finder object of the same shape as the image.
This actually creates many sub-finder objects, one for each \Octave\. Octave 1
has the same shape as the image. Octave 2 is twice smaller. Octave 3 is four
time smaller than Octave 1, etc. Optionally, you can create Octave 0 that is
twice bigger than Octave 1, but it takes a lot of memory and tracking results
are bad. So here we set Octave0=False.
The maximal scale at which particles are looked for is set by nbOctaves.

finder = track.MultiscaleBlobFinder(im.shape, Octave0=False, nbOctaves=4)
finder?

Feed the image in the tracker with default tracking parameters already does a
great job. the output has three columns : $(x,y,r,i)$ where $r$ is a first
approximation of the radius of the particle (see below) and $i$ is a measure of
the brightness of the particle.

The smallest particle that can be detected with the default parameter $k=1.6$ in
2D is about 3 pixels in radius. In 3D it would be 4 pixels in radius. To
increase this smallest scale you can increase the parameter $k$. Decreasing $k$
below 1.2 is probably not a good idear since you will detect noise as particles.
Redo your acquisition with higher resolution instead.

centers = finder(im, k=1.6)
print centers.shape
print "smallest particle detected has a radius of %g px"%(centers[:,-2].min()) 
draw_circles(centers[:,0], centers[:,1], centers[:,2], facecolor='none', edgecolor='g')
plt.imshow(im, 'hot');

(305, 4)
smallest particle detected has a radius of 0.00130704 px

However some small particles are missing, for example near the large particle at
the center. Maybe it is because by default the MultiscaleFinder removes
overlapping particles? Let us try to disable this removal.

centers = finder(im, removeOverlap=False)
draw_circles(centers[:,0], centers[:,1], centers[:,2], facecolor='none', edgecolor='g')
plt.imshow(im, 'hot');

Well, we gained only spurious detections.

We can also try to disable a filter that rejects local minima that are elongated
in space.

centers = finder(im, maxedge=-1)
draw_circles(centers[:,0], centers[:,1], centers[:,2], facecolor='none', edgecolor='g')
plt.imshow(im, 'hot');

That was it seemingly. Now we have all particles.

histR0, bins = np.histogram(centers[:,-2], bins=np.arange(30))
plt.step(bins[:-1], histR0);
plt.xlabel('radius (px)');
plt.ylabel('count');

For sanity, it is probably better to filter out the particles with a radius
smaller than 1 pixel.

centers = centers[centers[:,-2]>1]

Introspection

The intermediate steps of the algorithm are accessible. For example one can
access the octaves (lines in figure below) and their successively blured
versions of the original image.

#get maximum intensity to set color bar
m = max([oc.layersG.max() for oc in finder.octaves[1:]])
for o, oc in enumerate(finder.octaves[1:]):
    for l, lay in enumerate(oc.layersG):
        a = plt.subplot(len(finder.octaves)-1,len(oc.layersG),len(oc.layersG)*o + l +1)
        #hide ticks for clarity
        a.axes.get_xaxis().set_visible(False)
        a.axes.get_yaxis().set_visible(False)
        plt.imshow(lay, 'hot', vmin=0, vmax=m);

One can also access the difference of Gaussians. Here relevant values are
negative, so we inverse the colors and saturate at zero.

#get maximum intensity to set color bar
m = min([oc.layers.min() for oc in finder.octaves[1:]])
for o, oc in enumerate(finder.octaves[1:]):
    for l, lay in enumerate(-oc.layers):
        a = plt.subplot(len(finder.octaves)-1,len(oc.layers),len(oc.layers)*o + l +1)
        #hide ticks for clarity
        a.axes.get_xaxis().set_visible(False)
        a.axes.get_yaxis().set_visible(False)
        plt.imshow(lay, 'hot', vmin=0, vmax=-m);

Each OctaveFinder looks for local minima (very negative) in the difference of
Gaussians space. Local minima in understood relative to space $(x,y)$ and scale
$s$.
The job of the MultiscaleFinder is to coordinate the action of the Octaves to
return a coherent result.

From scales to sizes

The multiscale algorithm finds local minima in space and scale $s$. How can we
convert scales in actual sizes (particle radius $r$)?
If the particles are far apart, their respective spots do not overlap, so we can
use the formula

$ R = s \sqrt{\frac{2d\ln \alpha}{1-\alpha^{-2}}} $

where $d$ is the dimensionality of the image (here 2) and $\alpha=2^{1/n}$ with
$n$ the number of subdivisions in an octave (parameter nbLayers when creating
the MultiscaleFinder).

MultiscaleFinder actually does this conversion when returning its result.

But what if particles are close together? Then their respective spots overlap
and the scale in only indirectly related to the size. We need to take into
account the distance between particles and their relative brightnesses. The
first step is to revert to scales.

s = track.radius2sigma(centers[:,-2], dim=2)

Then we have to find the couples of particles whoes spots probably overlap. The
submodule colloids.particles has a function to do this.

from colloids.particles import get_bonds
bonds, dists = get_bonds(positions=centers[:,::2], radii=centers[:,-2], maxdist=3.0)

Now we have all the ingredients to run the reconstruction.

Note: You need boost libraries installed on your system to proceed.

sudo apt-get install libboost-all-dev

:::python
radii1 = track.global_rescale_intensity(s, bonds, dists, centers[:,-1])
draw_circles(centers[:,0], centers[:,1], radii1, facecolor='none', edgecolor='g')
plt.imshow(im, 'hot');

The radii where underestimated indeed!

histR1, bins = np.histogram(radii1, bins=np.arange(30))
plt.step(bins[:-1], histR0, label='supposed dilute');
plt.step(bins[:-1], histR1, label='corrected for overlap');
plt.xlabel('radius (px)');
plt.ylabel('count');
plt.legend(loc='upper right');

Recent changes to Multiscale

Multiscale modified by Lam Son

Multiscale modified by Lam Son

Multiscale modified by Lam Son

Multiscale modified by Lam Son

Multiscale localisation

Introspection

From scales to sizes