Tutorial about localizations per frame

from pathlib import Path

%matplotlib inline

import matplotlib.pyplot as plt

import locan as lc

lc.show_versions(system=False, dependencies=False, verbose=False)

Locan:
   version: 0.20.0.dev41+g755b969

Python:
   version: 3.11.6

Load rapidSTORM data file

Identify some data in the test_data directory and provide a path using pathlib.Path

path = lc.ROOT_DIR / 'tests/test_data/rapidSTORM_dstorm_data.txt'
print(path, '\n')

dat = lc.load_rapidSTORM_file(path=path, nrows=1000)

/home/docs/checkouts/readthedocs.org/user_builds/locan/envs/latest/lib/python3.11/site-packages/locan/tests/test_data/rapidSTORM_dstorm_data.txt 

Jupyter environment detected. Enabling Open3D WebVisualizer.
[Open3D INFO] WebRTC GUI backend enabled.
[Open3D INFO] WebRTCWindowSystem: HTTP handshake server disabled.

Print information about the data:

print(dat.data.head(), '\n')
print('Summary:')
dat.print_summary()
print('Properties:')
print(dat.properties)

   position_x  position_y  frame  intensity  chi_square  local_background
0     9657.40     24533.5      0   33290.10   1192250.0        767.732971
1    16754.90     18770.0      0   21275.40   2106810.0        875.460999
2    14457.60     18582.6      0   20748.70    526031.0        703.369995
3     6820.58     16662.8      0    8531.77   3179190.0        852.789001
4    19183.20     22907.2      0   14139.60    448631.0        662.770020 

Summary:
identifier: "1"
comment: ""
source: EXPERIMENT
state: RAW
element_count: 14
frame_count: 1
file {
  type: RAPIDSTORM
  path: "/home/docs/checkouts/readthedocs.org/user_builds/locan/envs/latest/lib/python3.11/site-packages/locan/tests/test_data/rapidSTORM_dstorm_data.txt"
}
creation_time {
  2024-03-14T11:07:44.308119Z
}

Properties:
{'localization_count': 14, 'position_x': 15873.847142857145, 'uncertainty_x': 2361.4490857013648, 'position_y': 17403.909285714286, 'uncertainty_y': 1803.9975262697349, 'intensity': 183987.66999999998, 'local_background': 675.0614, 'frame': 0, 'region_measure_bb': 730882123.3259, 'localization_density_bb': 1.915493559521281e-08, 'subregion_measure_bb': 108337.2}

Visualization

lc.render_2d(dat, bin_size=500, rescale=lc.Trafo.EQUALIZE_0P3);

Analyze localizations per frame

We have a look at the number of localizations that were detected in each frame.

The analysis class Localizations_per_frame provides numerical results, a plot of results versus frame, and a density graph (histogram).

lpf = lc.LocalizationsPerFrame()
lpf.compute(dat)

LocalizationsPerFrame(norm=None, time_delta=integration_time, resample=None)

lpf.results

<locan.analysis.localizations_per_frame._Results at 0x7f0a1c93c990>

print(lpf.results.time_series.head())

frame
0    14.0
Name: n_localizations, dtype: float64

The plot shows results smoothed by a running average according to the specified window.

lpf.plot(window=10);

The histogram per default provides automatic bins, is normalized to show a probability density function and estimates a normal distribution.

lpf.hist();

/home/docs/checkouts/readthedocs.org/user_builds/locan/envs/latest/lib/python3.11/site-packages/scipy/stats/_distn_infrastructure.py:2244: RuntimeWarning: invalid value encountered in multiply
  lower_bound = _a * scale + loc
/home/docs/checkouts/readthedocs.org/user_builds/locan/envs/latest/lib/python3.11/site-packages/scipy/stats/_distn_infrastructure.py:2245: RuntimeWarning: invalid value encountered in multiply
  upper_bound = _b * scale + loc

The accumulation time is the time at which fraction of the cumulative intensity is reached.

lpf.results.accumulation_time()

0

Plot normalized values

We can normalize the number of localizations to any other LocData property.

dat.properties

{'localization_count': 14,
 'position_x': 15873.847142857145,
 'uncertainty_x': 2361.4490857013648,
 'position_y': 17403.909285714286,
 'uncertainty_y': 1803.9975262697349,
 'intensity': 183987.66999999998,
 'local_background': 675.0614,
 'frame': 0,
 'region_measure_bb': 730882123.3259,
 'localization_density_bb': 1.915493559521281e-08,
 'subregion_measure_bb': 108337.2}

lpf = lc.LocalizationsPerFrame(norm='region_measure_bb').compute(dat)

lpf.hist();

/home/docs/checkouts/readthedocs.org/user_builds/locan/envs/latest/lib/python3.11/site-packages/scipy/stats/_distn_infrastructure.py:2244: RuntimeWarning: invalid value encountered in multiply
  lower_bound = _a * scale + loc
/home/docs/checkouts/readthedocs.org/user_builds/locan/envs/latest/lib/python3.11/site-packages/scipy/stats/_distn_infrastructure.py:2245: RuntimeWarning: invalid value encountered in multiply
  upper_bound = _b * scale + loc