4. Coupling datasets#

[1]:

from pathlib2 import Path
import papylio as pp
import matplotlib.pyplot as plt

%matplotlib inline

Experiment import#

Note that the sequencing data is automatically imported.

[2]:

experiment_path = Path(r'C:\Users\user\Desktop\SPARXS example dataset')

[3]:

exp = pp.Experiment(experiment_path)

Import files: 100%|██████████████████████████████████████████████████████████████| 4190/4190 [00:00<00:00, 6337.52it/s]


File(Single-molecule data - bead slide\Bead slide TIRF 561 001) used as mapping

Initialize experiment:
C:\Users\user\Desktop\SPARXS example dataset

Import sequencing data:
Sequencing data\sequencing_data.nc

[4]:

files_bead_slide = exp.files.select('Bead slide', 'name')
files_green_laser = exp.files.select('Single-molecule data - green laser', 'relativePath')
files_red_laser_before = exp.files.select('Single-molecule data - red laser before', 'relativePath')
files_red_laser_after = exp.files.select('Single-molecule data - red laser after', 'relativePath')

[5]:

files_red_laser_before.movie.illumination_arrangement = [1]
files_red_laser_after.movie.illumination_arrangement = [1]

Add sequencing data to file datasets#

Here we import the matched sequences in the dataset for each field of view.

[6]:

files_green_laser.insert_sequencing_data_into_file_dataset(include_raw_sequences=True, include_aligned_sequences=True,
                                                           include_sequence_subset=True)

  0%|                                                                                          | 0/896 [00:00<?, ?it/s]

Serial processing

100%|████████████████████████████████████████████████████████████████████████████████| 896/896 [02:11<00:00,  6.82it/s]

include_raw_sequences If True, include the ‘raw’ unaligned sequences in the file dataset.

include_aligned_sequences If True, include the aligned sequences in the file dataset.

include_sequence_subset If True, include the sequence subset in the file dataset.

[7]:

files_green_laser[500].dataset

[7]:

<xarray.Dataset>
Dimensions:                   (molecule: 1715, channel: 2, dimension: 2,
                               frame: 400)
Coordinates:
    molecule_in_file          (molecule) int32 0 1 2 3 4 ... 1711 1712 1713 1714
    file                      (molecule) |S58 b'Single-molecule data - green ...
  * channel                   (channel) int64 0 1
  * dimension                 (dimension) |S1 b'x' b'y'
    time                      (frame) float64 0.0 0.121 0.244 ... 48.75 48.87
  * frame                     (frame) int32 0 1 2 3 4 5 ... 395 396 397 398 399
    illumination              (frame) int32 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0
    sequence_in_file          (molecule) int32 -1 -1 -1 -1 744 ... -1 -1 -1 -1
Dimensions without coordinates: molecule
Data variables: (12/16)
    selected                  (molecule) bool False False False ... False False
    coordinates               (molecule, channel, dimension) float64 243.9 .....
    intensity                 (molecule, channel, frame) float64 2.898e+04 .....
    intensity_raw             (molecule, channel, frame) float64 1.81e+04 ......
    FRET                      (molecule, frame) float64 0.2133 0.1391 ... 0.6694
    intensity_red_before      (molecule, channel) float64 52.21 ... -318.6
    ...                        ...
    sequence_quality          (molecule) |S147 b'                            ...
    sequence_aligned          (molecule) |S147 b'----------------------------...
    sequence_quality_aligned  (molecule) |S147 b'                            ...
    sequence_subset           (molecule) |S8 b'--------' ... b'--------'
    sequence_quality_subset   (molecule) |S8 b'        ' ... b'        '
    sequence_coordinates      (molecule, dimension) int64 0 0 0 0 0 ... 0 0 0 0

xarray.Dataset

Dimensions:
- molecule: 1715
- channel: 2
- dimension: 2
- frame: 400

Coordinates: (8)

molecule_in_file
(molecule)
int32
0 1 2 3 4 ... 1711 1712 1713 1714
```
array([   0,    1,    2, ..., 1712, 1713, 1714])
```

file

(molecule)

|S58

b'Single-molecule data - green l...

array([b'Single-molecule data - green laser - 501-600\\TIRF 561 0501',
       b'Single-molecule data - green laser - 501-600\\TIRF 561 0501',
       b'Single-molecule data - green laser - 501-600\\TIRF 561 0501',
       ...,
       b'Single-molecule data - green laser - 501-600\\TIRF 561 0501',
       b'Single-molecule data - green laser - 501-600\\TIRF 561 0501',
       b'Single-molecule data - green laser - 501-600\\TIRF 561 0501'],
      dtype='|S58')

channel
(channel)
int64
0 1
```
array([0, 1], dtype=int64)
```
dimension
(dimension)
|S1
b'x' b'y'
```
array([b'x', b'y'], dtype='|S1')
```

time

(frame)

float64

0.0 0.121 0.244 ... 48.75 48.87

units :: s

array([ 0.   ,  0.121,  0.244,  0.367,  0.489,  0.612,  0.734,  0.856,
        0.979,  1.102,  1.224,  1.346,  1.469,  1.591,  1.714,  1.837,
        1.959,  2.081,  2.204,  2.326,  2.449,  2.572,  2.693,  2.816,
        2.939,  3.061,  3.184,  3.306,  3.428,  3.551,  3.674,  3.796,
        3.919,  4.041,  4.163,  4.286,  4.409,  4.532,  4.653,  4.776,
        4.899,  5.021,  5.144,  5.266,  5.388,  5.511,  5.634,  5.756,
        5.878,  6.001,  6.123,  6.246,  6.369,  6.49 ,  6.613,  6.736,
        6.858,  6.981,  7.103,  7.225,  7.348,  7.471,  7.593,  7.716,
        7.838,  7.96 ,  8.083,  8.206,  8.328,  8.45 ,  8.573,  8.695,
        8.818,  8.941,  9.062,  9.185,  9.308,  9.43 ,  9.553,  9.676,
        9.797,  9.92 , 10.043, 10.165, 10.288, 10.41 , 10.532, 10.655,
       10.778, 10.9  , 11.022, 11.145, 11.267, 11.39 , 11.513, 11.635,
       11.757, 11.88 , 12.003, 12.125, 12.248, 12.37 , 12.492, 12.615,
       12.738, 12.86 , 12.982, 13.105, 13.227, 13.35 , 13.473, 13.594,
       13.717, 13.84 , 13.962, 14.085, 14.207, 14.329, 14.452, 14.575,
       14.697, 14.819, 14.942, 15.064, 15.187, 15.31 , 15.431, 15.554,
       15.677, 15.799, 15.922, 16.045, 16.166, 16.289, 16.412, 16.534,
       16.657, 16.779, 16.901, 17.024, 17.147, 17.269, 17.391, 17.514,
       17.636, 17.759, 17.882, 18.004, 18.126, 18.249, 18.372, 18.494,
       18.617, 18.739, 18.861, 18.984, 19.107, 19.229, 19.351, 19.474,
...
       29.395, 29.517, 29.639, 29.762, 29.885, 30.008, 30.13 , 30.252,
       30.375, 30.497, 30.62 , 30.743, 30.864, 30.987, 31.11 , 31.232,
       31.355, 31.477, 31.599, 31.722, 31.845, 31.967, 32.089, 32.212,
       32.334, 32.457, 32.58 , 32.701, 32.824, 32.947, 33.069, 33.192,
       33.315, 33.436, 33.559, 33.682, 33.804, 33.927, 34.049, 34.171,
       34.294, 34.417, 34.539, 34.661, 34.784, 34.906, 35.029, 35.152,
       35.273, 35.396, 35.519, 35.642, 35.764, 35.887, 36.009, 36.131,
       36.254, 36.377, 36.499, 36.621, 36.744, 36.866, 36.989, 37.112,
       37.233, 37.356, 37.479, 37.601, 37.724, 37.846, 37.968, 38.091,
       38.214, 38.336, 38.458, 38.581, 38.703, 38.826, 38.949, 39.071,
       39.193, 39.316, 39.438, 39.561, 39.684, 39.805, 39.928, 40.051,
       40.173, 40.296, 40.418, 40.54 , 40.663, 40.786, 40.908, 41.031,
       41.153, 41.275, 41.398, 41.521, 41.643, 41.765, 41.888, 42.01 ,
       42.133, 42.256, 42.378, 42.5  , 42.623, 42.746, 42.868, 42.99 ,
       43.113, 43.235, 43.358, 43.481, 43.602, 43.725, 43.848, 43.97 ,
       44.093, 44.216, 44.337, 44.46 , 44.583, 44.705, 44.828, 44.95 ,
       45.072, 45.195, 45.318, 45.44 , 45.563, 45.685, 45.807, 45.93 ,
       46.053, 46.175, 46.297, 46.42 , 46.542, 46.665, 46.788, 46.909,
       47.032, 47.155, 47.277, 47.4  , 47.523, 47.644, 47.767, 47.89 ,
       48.012, 48.135, 48.257, 48.379, 48.502, 48.625, 48.747, 48.869])

frame
(frame)
int32
0 1 2 3 4 5 ... 395 396 397 398 399
```
array([  0,   1,   2, ..., 397, 398, 399])
```

illumination

(frame)

int32

0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0

array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0])

sequence_in_file
(molecule)
int32
-1 -1 -1 -1 744 ... 228 -1 -1 -1 -1
```
array([-1, -1, -1, ..., -1, -1, -1])
```

Data variables: (16)

selected
(molecule)
bool
False False False ... False False
```
array([False, False, False, ..., False, False, False])
```

coordinates

(molecule, channel, dimension)

float64

243.9 61.89 502.1 ... 418.3 77.39

array([[[243.93597622,  61.88795777],
        [502.12243079,  60.11963717]],

       [[166.11888704,  91.33992172],
        [424.4910416 ,  89.56399082]],

       [[100.70313181, 137.16362314],
        [359.43187626, 135.33031307]],

       ...,

       [[179.88167693, 129.19692491],
        [438.12714842, 127.33278696]],

       [[166.89322425, 316.3760238 ],
        [425.02396582, 314.12359985]],

       [[159.86694686,  79.13934833],
        [418.29037807,  77.39065092]]])

intensity

(molecule, channel, frame)

float64

2.898e+04 3.158e+04 ... -2.066e+03

background_correction :: [-300 -100]
gamma_correction :: 1.5
alpha_correction :: 0.05

array([[[28975.97227059, 31580.00782344, 32614.46511028, ...,
         27713.09534019, 18902.4053957 , 18615.01418201],
        [ 7856.32431185,  5104.66630725, 10642.30933833, ...,
          5002.83909417, 10344.1440267 , 10556.69203597]],

       [[15493.28816622, 13474.11362244,  8778.92220836, ...,
         10595.31994378, 11164.34204   , 10596.84833099],
        [12312.35617901, 12985.51965608, 13285.85387414, ...,
          9638.89491729, 10376.03105074, 12897.55429275]],

       [[ 8831.64117126,  4886.00151843,  5391.84868229, ...,
         11972.75317319, 13077.07842652, 16182.08074911],
        [ 7804.6098217 , 13823.44885838, 12263.87785515, ...,
         -3086.90507183, -1187.01787197,  -188.81077161]],

       ...,

       [[20777.30955943, 16343.40229168, 17795.81041354, ...,
         18273.36211846, 16340.95374724, 15943.8535936 ],
        [ 1319.23573918,  1920.10596601,  -344.4333578 , ...,
         -2897.44659654,   579.79353219,   891.13655644]],

       [[24065.44155189, 24211.63512206, 26465.09742933, ...,
         10191.50409444, 11988.24787106, 10176.55391391],
        [ 2363.22145245,  2370.83790745,  2599.66260594, ...,
          3022.1389737 ,   405.0688531 ,  1122.5420595 ]],

       [[20866.42959906, 16662.70214387, 18479.9853852 , ...,
         -1981.20665671, -3071.92275343, -1020.31834956],
        [ -212.07637597,  -883.91587396, -1803.26307486, ...,
          1895.98240637,  -526.70276168, -2066.20654648]]])

intensity_raw

(molecule, channel, frame)

float64

1.81e+04 1.975e+04 ... -2.217e+03

array([[[18097.44271149, 19750.79861805, 20407.59689542, ...,
         17295.61608901, 11701.52723536, 11519.0566235 ],
        [ 9205.12292538,  6583.66669842, 12173.03259385, ...,
          6288.49386118, 11189.26429648, 11387.44274507]],

       [[ 9537.00835951,  8254.99277615,  5273.91886245, ...,
          6427.18726589,  6788.47113651,  6428.15767047],
        [12987.02058732, 13559.2253372 , 13624.79998455, ...,
         10068.66091448, 10834.24815274, 13327.3967093 ]],

       [[ 5307.39121985,  2802.2231863 ,  3123.39598876, ...,
          7301.74804647,  8002.90693748,  9974.33698356],
        [ 8146.19188026, 13967.7489343 , 12433.47028926, ...,
         -2588.26741317,  -633.16395064,   520.29326584]],

       ...,

       [[12891.94257742, 10076.7633598 , 10998.92724669, ...,
         11302.13467839, 10075.2087284 ,  9823.08164673],
        [ 2258.10121715,  2637.2760806 ,   445.35716288, ...,
         -2083.77849062,  1296.84121955,  1588.32923612]],

       [[14979.64542977, 15072.46674416, 16503.23646307, ...,
          6170.79625044,  7311.58594988,  6161.30407232],
        [ 3466.49353004,  3481.41966355,  3822.9174774 , ...,
          3431.71417843,   904.48124665,  1531.36975519]],

       [[12948.52672956, 10279.49342468, 11433.32405409, ...,
         -1557.90898839, -2250.42714504,  -947.82117433],
        [  731.24510398,  -150.78076677,  -979.2638056 , ...,
          1696.92207353,  -780.29889935, -2217.22246396]]])

FRET

(molecule, frame)

float64

0.2133 0.1391 ... 0.1464 0.6694

array([[0.21329988, 0.13914983, 0.24602642, ..., 0.15291751, 0.35368767,
        0.3618812 ],
       [0.44280061, 0.49076718, 0.60212956, ..., 0.47636614, 0.48170155,
        0.54896285],
       [0.46913273, 0.73884847, 0.69461191, ..., 0.        , 0.        ,
        0.        ],
       ...,
       [0.05970326, 0.10513347, 0.        , ..., 0.        , 0.03426524,
        0.0529336 ],
       [0.08941888, 0.08918801, 0.0894438 , ..., 0.22871353, 0.03268446,
        0.09934795],
       [0.        , 0.        , 0.        , ..., 0.        , 0.1463622 ,
        0.66942812]])

intensity_red_before

(molecule, channel)

float64

52.21 1.292e+04 ... -46.74 -318.6

array([[ 5.22145577e+01,  1.29150144e+04],
       [ 7.62973119e+01,  1.05695470e+04],
       [ 3.06469347e+01,  7.96314915e+03],
       ...,
       [-5.01300830e+01, -3.24341307e+02],
       [-5.52651812e+00,  7.12210532e+03],
       [-4.67424667e+01, -3.18552437e+02]])

intensity_red_after

(molecule, channel)

float64

14.35 1.332e+04 ... -15.46 -153.9

array([[ 1.43520548e+01,  1.33210147e+04],
       [ 4.45319845e+01,  1.03992635e+04],
       [-6.08210607e+01, -4.59597027e+02],
       ...,
       [ 2.47540571e+01, -3.94519334e+02],
       [-8.38917790e+00,  5.09300219e+02],
       [-1.54638723e+01, -1.53913515e+02]])

sequence_name
(molecule)
|S10
b'' b'' b'' b'' ... b'' b'' b'' b''
```
array([b'', b'', b'', ..., b'', b'', b''], dtype='|S10')
```
sequence_tile
(molecule)
int64
0 0 0 0 1102 0 0 ... 0 1102 0 0 0 0
```
array([0, 0, 0, ..., 0, 0, 0], dtype=int64)
```

sequence

(molecule)

|S147

b'------------------------------...

array([b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       ...,
       b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       b'---------------------------------------------------------------------------------------------------------------------------------------------------'],
      dtype='|S147')

sequence_quality

(molecule)

|S147

b' ...

array([b'                                                                                                                                                   ',
       b'                                                                                                                                                   ',
       b'                                                                                                                                                   ',
       ...,
       b'                                                                                                                                                   ',
       b'                                                                                                                                                   ',
       b'                                                                                                                                                   '],
      dtype='|S147')

sequence_aligned

(molecule)

|S147

b'------------------------------...

array([b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       ...,
       b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       b'---------------------------------------------------------------------------------------------------------------------------------------------------'],
      dtype='|S147')

sequence_quality_aligned

(molecule)

|S147

b' ...

array([b'                                                                                                                                                   ',
       b'                                                                                                                                                   ',
       b'                                                                                                                                                   ',
       ...,
       b'                                                                                                                                                   ',
       b'                                                                                                                                                   ',
       b'                                                                                                                                                   '],
      dtype='|S147')

sequence_subset

(molecule)

|S8

b'--------' ... b'--------'

array([b'--------', b'--------', b'--------', ..., b'--------',
       b'--------', b'--------'], dtype='|S8')

sequence_quality_subset

(molecule)

|S8

b' ' ... b' '

array([b'        ', b'        ', b'        ', ..., b'        ',
       b'        ', b'        '], dtype='|S8')

sequence_coordinates

(molecule, dimension)

int64

0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0

array([[0, 0],
       [0, 0],
       [0, 0],
       ...,
       [0, 0],
       [0, 0],
       [0, 0]], dtype=int64)

Indexes: (3)

channel

PandasIndex

PandasIndex(Int64Index([0, 1], dtype='int64', name='channel'))

dimension

PandasIndex

PandasIndex(Index([b'x', b'y'], dtype='object', name='dimension'))

frame

PandasIndex

PandasIndex(Int64Index([  0,   1,   2,   3,   4,   5,   6,   7,   8,   9,
            ...
            390, 391, 392, 393, 394, 395, 396, 397, 398, 399],
           dtype='int64', name='frame', length=400))

Attributes: (0)

The dataset of each movie is expanded with several sequence variables.

Merge and reorder datasets#

Select files that have a sequencing alignment

[8]:

files = files_green_laser[files_green_laser.has_sequencing_match]

To create a single large dataset

[9]:

# files.merge_datasets(filepath_out=exp.main_path / 'Analysis' / 'complete_dataset.nc', init_file_index=-1,
#                               with_sequence_only=True)

To create dataset for each sequence subset

[10]:

files.reorder_datasets_using_sequence_subset(folderpath_out=exp.main_path / 'Analysis' / 'Datasets per sequence')

100%|████████████████████████████████████████████████████████████████████████████████████████| 744/744 [00:00<?, ?it/s]

Serial processing

100%|████████████████████████████████████████████████████████████████████████████████| 744/744 [20:52<00:00,  1.68s/it]

[11]:

files[395].dataset

[11]:

<xarray.Dataset>
Dimensions:                   (molecule: 1715, channel: 2, dimension: 2,
                               frame: 400)
Coordinates:
    molecule_in_file          (molecule) int32 0 1 2 3 4 ... 1711 1712 1713 1714
    file                      (molecule) |S58 b'Single-molecule data - green ...
  * channel                   (channel) int64 0 1
  * dimension                 (dimension) |S1 b'x' b'y'
    time                      (frame) float64 0.0 0.121 0.244 ... 48.75 48.87
  * frame                     (frame) int32 0 1 2 3 4 5 ... 395 396 397 398 399
    illumination              (frame) int32 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0
    sequence_in_file          (molecule) int32 -1 -1 -1 -1 744 ... -1 -1 -1 -1
Dimensions without coordinates: molecule
Data variables: (12/16)
    selected                  (molecule) bool False False False ... False False
    coordinates               (molecule, channel, dimension) float64 243.9 .....
    intensity                 (molecule, channel, frame) float64 2.898e+04 .....
    intensity_raw             (molecule, channel, frame) float64 1.81e+04 ......
    FRET                      (molecule, frame) float64 0.2133 0.1391 ... 0.6694
    intensity_red_before      (molecule, channel) float64 52.21 ... -318.6
    ...                        ...
    sequence_quality          (molecule) |S147 b'                            ...
    sequence_aligned          (molecule) |S147 b'----------------------------...
    sequence_quality_aligned  (molecule) |S147 b'                            ...
    sequence_subset           (molecule) |S8 b'--------' ... b'--------'
    sequence_quality_subset   (molecule) |S8 b'        ' ... b'        '
    sequence_coordinates      (molecule, dimension) int64 0 0 0 0 0 ... 0 0 0 0

xarray.Dataset

Dimensions:
- molecule: 1715
- channel: 2
- dimension: 2
- frame: 400

Coordinates: (8)

molecule_in_file
(molecule)
int32
0 1 2 3 4 ... 1711 1712 1713 1714
```
array([   0,    1,    2, ..., 1712, 1713, 1714])
```

file

(molecule)

|S58

b'Single-molecule data - green l...

array([b'Single-molecule data - green laser - 501-600\\TIRF 561 0501',
       b'Single-molecule data - green laser - 501-600\\TIRF 561 0501',
       b'Single-molecule data - green laser - 501-600\\TIRF 561 0501',
       ...,
       b'Single-molecule data - green laser - 501-600\\TIRF 561 0501',
       b'Single-molecule data - green laser - 501-600\\TIRF 561 0501',
       b'Single-molecule data - green laser - 501-600\\TIRF 561 0501'],
      dtype='|S58')

channel
(channel)
int64
0 1
```
array([0, 1], dtype=int64)
```
dimension
(dimension)
|S1
b'x' b'y'
```
array([b'x', b'y'], dtype='|S1')
```

time

(frame)

float64

0.0 0.121 0.244 ... 48.75 48.87

units :: s

array([ 0.   ,  0.121,  0.244,  0.367,  0.489,  0.612,  0.734,  0.856,
        0.979,  1.102,  1.224,  1.346,  1.469,  1.591,  1.714,  1.837,
        1.959,  2.081,  2.204,  2.326,  2.449,  2.572,  2.693,  2.816,
        2.939,  3.061,  3.184,  3.306,  3.428,  3.551,  3.674,  3.796,
        3.919,  4.041,  4.163,  4.286,  4.409,  4.532,  4.653,  4.776,
        4.899,  5.021,  5.144,  5.266,  5.388,  5.511,  5.634,  5.756,
        5.878,  6.001,  6.123,  6.246,  6.369,  6.49 ,  6.613,  6.736,
        6.858,  6.981,  7.103,  7.225,  7.348,  7.471,  7.593,  7.716,
        7.838,  7.96 ,  8.083,  8.206,  8.328,  8.45 ,  8.573,  8.695,
        8.818,  8.941,  9.062,  9.185,  9.308,  9.43 ,  9.553,  9.676,
        9.797,  9.92 , 10.043, 10.165, 10.288, 10.41 , 10.532, 10.655,
       10.778, 10.9  , 11.022, 11.145, 11.267, 11.39 , 11.513, 11.635,
       11.757, 11.88 , 12.003, 12.125, 12.248, 12.37 , 12.492, 12.615,
       12.738, 12.86 , 12.982, 13.105, 13.227, 13.35 , 13.473, 13.594,
       13.717, 13.84 , 13.962, 14.085, 14.207, 14.329, 14.452, 14.575,
       14.697, 14.819, 14.942, 15.064, 15.187, 15.31 , 15.431, 15.554,
       15.677, 15.799, 15.922, 16.045, 16.166, 16.289, 16.412, 16.534,
       16.657, 16.779, 16.901, 17.024, 17.147, 17.269, 17.391, 17.514,
       17.636, 17.759, 17.882, 18.004, 18.126, 18.249, 18.372, 18.494,
       18.617, 18.739, 18.861, 18.984, 19.107, 19.229, 19.351, 19.474,
...
       29.395, 29.517, 29.639, 29.762, 29.885, 30.008, 30.13 , 30.252,
       30.375, 30.497, 30.62 , 30.743, 30.864, 30.987, 31.11 , 31.232,
       31.355, 31.477, 31.599, 31.722, 31.845, 31.967, 32.089, 32.212,
       32.334, 32.457, 32.58 , 32.701, 32.824, 32.947, 33.069, 33.192,
       33.315, 33.436, 33.559, 33.682, 33.804, 33.927, 34.049, 34.171,
       34.294, 34.417, 34.539, 34.661, 34.784, 34.906, 35.029, 35.152,
       35.273, 35.396, 35.519, 35.642, 35.764, 35.887, 36.009, 36.131,
       36.254, 36.377, 36.499, 36.621, 36.744, 36.866, 36.989, 37.112,
       37.233, 37.356, 37.479, 37.601, 37.724, 37.846, 37.968, 38.091,
       38.214, 38.336, 38.458, 38.581, 38.703, 38.826, 38.949, 39.071,
       39.193, 39.316, 39.438, 39.561, 39.684, 39.805, 39.928, 40.051,
       40.173, 40.296, 40.418, 40.54 , 40.663, 40.786, 40.908, 41.031,
       41.153, 41.275, 41.398, 41.521, 41.643, 41.765, 41.888, 42.01 ,
       42.133, 42.256, 42.378, 42.5  , 42.623, 42.746, 42.868, 42.99 ,
       43.113, 43.235, 43.358, 43.481, 43.602, 43.725, 43.848, 43.97 ,
       44.093, 44.216, 44.337, 44.46 , 44.583, 44.705, 44.828, 44.95 ,
       45.072, 45.195, 45.318, 45.44 , 45.563, 45.685, 45.807, 45.93 ,
       46.053, 46.175, 46.297, 46.42 , 46.542, 46.665, 46.788, 46.909,
       47.032, 47.155, 47.277, 47.4  , 47.523, 47.644, 47.767, 47.89 ,
       48.012, 48.135, 48.257, 48.379, 48.502, 48.625, 48.747, 48.869])

frame
(frame)
int32
0 1 2 3 4 5 ... 395 396 397 398 399
```
array([  0,   1,   2, ..., 397, 398, 399])
```

illumination

(frame)

int32

0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0

array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0])

sequence_in_file
(molecule)
int32
-1 -1 -1 -1 744 ... 228 -1 -1 -1 -1
```
array([-1, -1, -1, ..., -1, -1, -1])
```

Data variables: (16)

selected
(molecule)
bool
False False False ... False False
```
array([False, False, False, ..., False, False, False])
```

coordinates

(molecule, channel, dimension)

float64

243.9 61.89 502.1 ... 418.3 77.39

array([[[243.93597622,  61.88795777],
        [502.12243079,  60.11963717]],

       [[166.11888704,  91.33992172],
        [424.4910416 ,  89.56399082]],

       [[100.70313181, 137.16362314],
        [359.43187626, 135.33031307]],

       ...,

       [[179.88167693, 129.19692491],
        [438.12714842, 127.33278696]],

       [[166.89322425, 316.3760238 ],
        [425.02396582, 314.12359985]],

       [[159.86694686,  79.13934833],
        [418.29037807,  77.39065092]]])

intensity

(molecule, channel, frame)

float64

2.898e+04 3.158e+04 ... -2.066e+03

background_correction :: [-300 -100]
gamma_correction :: 1.5
alpha_correction :: 0.05

array([[[28975.97227059, 31580.00782344, 32614.46511028, ...,
         27713.09534019, 18902.4053957 , 18615.01418201],
        [ 7856.32431185,  5104.66630725, 10642.30933833, ...,
          5002.83909417, 10344.1440267 , 10556.69203597]],

       [[15493.28816622, 13474.11362244,  8778.92220836, ...,
         10595.31994378, 11164.34204   , 10596.84833099],
        [12312.35617901, 12985.51965608, 13285.85387414, ...,
          9638.89491729, 10376.03105074, 12897.55429275]],

       [[ 8831.64117126,  4886.00151843,  5391.84868229, ...,
         11972.75317319, 13077.07842652, 16182.08074911],
        [ 7804.6098217 , 13823.44885838, 12263.87785515, ...,
         -3086.90507183, -1187.01787197,  -188.81077161]],

       ...,

       [[20777.30955943, 16343.40229168, 17795.81041354, ...,
         18273.36211846, 16340.95374724, 15943.8535936 ],
        [ 1319.23573918,  1920.10596601,  -344.4333578 , ...,
         -2897.44659654,   579.79353219,   891.13655644]],

       [[24065.44155189, 24211.63512206, 26465.09742933, ...,
         10191.50409444, 11988.24787106, 10176.55391391],
        [ 2363.22145245,  2370.83790745,  2599.66260594, ...,
          3022.1389737 ,   405.0688531 ,  1122.5420595 ]],

       [[20866.42959906, 16662.70214387, 18479.9853852 , ...,
         -1981.20665671, -3071.92275343, -1020.31834956],
        [ -212.07637597,  -883.91587396, -1803.26307486, ...,
          1895.98240637,  -526.70276168, -2066.20654648]]])

intensity_raw

(molecule, channel, frame)

float64

1.81e+04 1.975e+04 ... -2.217e+03

array([[[18097.44271149, 19750.79861805, 20407.59689542, ...,
         17295.61608901, 11701.52723536, 11519.0566235 ],
        [ 9205.12292538,  6583.66669842, 12173.03259385, ...,
          6288.49386118, 11189.26429648, 11387.44274507]],

       [[ 9537.00835951,  8254.99277615,  5273.91886245, ...,
          6427.18726589,  6788.47113651,  6428.15767047],
        [12987.02058732, 13559.2253372 , 13624.79998455, ...,
         10068.66091448, 10834.24815274, 13327.3967093 ]],

       [[ 5307.39121985,  2802.2231863 ,  3123.39598876, ...,
          7301.74804647,  8002.90693748,  9974.33698356],
        [ 8146.19188026, 13967.7489343 , 12433.47028926, ...,
         -2588.26741317,  -633.16395064,   520.29326584]],

       ...,

       [[12891.94257742, 10076.7633598 , 10998.92724669, ...,
         11302.13467839, 10075.2087284 ,  9823.08164673],
        [ 2258.10121715,  2637.2760806 ,   445.35716288, ...,
         -2083.77849062,  1296.84121955,  1588.32923612]],

       [[14979.64542977, 15072.46674416, 16503.23646307, ...,
          6170.79625044,  7311.58594988,  6161.30407232],
        [ 3466.49353004,  3481.41966355,  3822.9174774 , ...,
          3431.71417843,   904.48124665,  1531.36975519]],

       [[12948.52672956, 10279.49342468, 11433.32405409, ...,
         -1557.90898839, -2250.42714504,  -947.82117433],
        [  731.24510398,  -150.78076677,  -979.2638056 , ...,
          1696.92207353,  -780.29889935, -2217.22246396]]])

FRET

(molecule, frame)

float64

0.2133 0.1391 ... 0.1464 0.6694

array([[0.21329988, 0.13914983, 0.24602642, ..., 0.15291751, 0.35368767,
        0.3618812 ],
       [0.44280061, 0.49076718, 0.60212956, ..., 0.47636614, 0.48170155,
        0.54896285],
       [0.46913273, 0.73884847, 0.69461191, ..., 0.        , 0.        ,
        0.        ],
       ...,
       [0.05970326, 0.10513347, 0.        , ..., 0.        , 0.03426524,
        0.0529336 ],
       [0.08941888, 0.08918801, 0.0894438 , ..., 0.22871353, 0.03268446,
        0.09934795],
       [0.        , 0.        , 0.        , ..., 0.        , 0.1463622 ,
        0.66942812]])

intensity_red_before

(molecule, channel)

float64

52.21 1.292e+04 ... -46.74 -318.6

array([[ 5.22145577e+01,  1.29150144e+04],
       [ 7.62973119e+01,  1.05695470e+04],
       [ 3.06469347e+01,  7.96314915e+03],
       ...,
       [-5.01300830e+01, -3.24341307e+02],
       [-5.52651812e+00,  7.12210532e+03],
       [-4.67424667e+01, -3.18552437e+02]])

intensity_red_after

(molecule, channel)

float64

14.35 1.332e+04 ... -15.46 -153.9

array([[ 1.43520548e+01,  1.33210147e+04],
       [ 4.45319845e+01,  1.03992635e+04],
       [-6.08210607e+01, -4.59597027e+02],
       ...,
       [ 2.47540571e+01, -3.94519334e+02],
       [-8.38917790e+00,  5.09300219e+02],
       [-1.54638723e+01, -1.53913515e+02]])

sequence_name
(molecule)
|S10
b'' b'' b'' b'' ... b'' b'' b'' b''
```
array([b'', b'', b'', ..., b'', b'', b''], dtype='|S10')
```
sequence_tile
(molecule)
int64
0 0 0 0 1102 0 0 ... 0 1102 0 0 0 0
```
array([0, 0, 0, ..., 0, 0, 0], dtype=int64)
```

sequence

(molecule)

|S147

b'------------------------------...

array([b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       ...,
       b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       b'---------------------------------------------------------------------------------------------------------------------------------------------------'],
      dtype='|S147')

sequence_quality

(molecule)

|S147

b' ...

array([b'                                                                                                                                                   ',
       b'                                                                                                                                                   ',
       b'                                                                                                                                                   ',
       ...,
       b'                                                                                                                                                   ',
       b'                                                                                                                                                   ',
       b'                                                                                                                                                   '],
      dtype='|S147')

sequence_aligned

(molecule)

|S147

b'------------------------------...

array([b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       ...,
       b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       b'---------------------------------------------------------------------------------------------------------------------------------------------------',
       b'---------------------------------------------------------------------------------------------------------------------------------------------------'],
      dtype='|S147')

sequence_quality_aligned

(molecule)

|S147

b' ...

array([b'                                                                                                                                                   ',
       b'                                                                                                                                                   ',
       b'                                                                                                                                                   ',
       ...,
       b'                                                                                                                                                   ',
       b'                                                                                                                                                   ',
       b'                                                                                                                                                   '],
      dtype='|S147')

sequence_subset

(molecule)

|S8

b'--------' ... b'--------'

array([b'--------', b'--------', b'--------', ..., b'--------',
       b'--------', b'--------'], dtype='|S8')

sequence_quality_subset

(molecule)

|S8

b' ' ... b' '

array([b'        ', b'        ', b'        ', ..., b'        ',
       b'        ', b'        '], dtype='|S8')

sequence_coordinates

(molecule, dimension)

int64

0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0

array([[0, 0],
       [0, 0],
       [0, 0],
       ...,
       [0, 0],
       [0, 0],
       [0, 0]], dtype=int64)

Indexes: (3)

channel

PandasIndex

PandasIndex(Int64Index([0, 1], dtype='int64', name='channel'))

dimension

PandasIndex

PandasIndex(Index([b'x', b'y'], dtype='object', name='dimension'))

frame

PandasIndex

PandasIndex(Int64Index([  0,   1,   2,   3,   4,   5,   6,   7,   8,   9,
            ...
            390, 391, 392, 393, 394, 395, 396, 397, 398, 399],
           dtype='int64', name='frame', length=400))

Attributes: (0)

4. Coupling datasets

Contents

4. Coupling datasets#

Experiment import#

Add sequencing data to file datasets#

Merge and reorder datasets#