Complete analysis with Skan

In this notebook, we reproduce the analysis leading to Figure 2 of our paper, submitted to PeerJ.

0. Getting the data

First, we need to download the input data, which is posted at the Open Science Framework (OSF) as a zip file. Many thanks to the OSF for providing hosting for scientific data. The data be downloaded at this URL:

https://osf.io/7vyx3

Download and extract the zipfile, and make sure the schizonts folder contained within it is placed in this notebook’s working directory.

1. Using skan.pipe to get a branch dataset for analysis

from glob import glob


schizont_files = glob('schizonts/*.tif')
# remove files ending with '01.tif', which are low-res overview images
schizont_files = list(filter(lambda x: not x.endswith('01.tif'),
                             schizont_files))

len(schizont_files)

96

Now we process all 96 images. This should take about a minute on a modern laptop, but could be faster on a multicore machine, as it processes images using as many CPUs as are avaliable.

from skan import pipe
import toolz as tz


data, per_image_data = tz.last(pipe.process_images(
    schizont_files,
    image_format='fei',
    threshold_radius=5e-8,
    smooth_radius=0.1,
    brightness_offset=0.075,
    scale_metadata_path='Scan/PixelHeight',
    crop_radius=20,
    smooth_method='Gaussian'
))

Next, we use the filename to infer the infection status of each image.

def infection_status(filename):
    if 'Uninf' in filename:
        return 'normal'
    else:
        return 'infected'


data['infection'] = data['filename'].apply(infection_status)

Also encoded in the filename are the cell number (unique by infection status) and the field number (each cell membrane is imaged at several non-overlapping locations).

import re  # regular expressions, for text matching


def cell_number(filename):
    regex = r'.*RBC(\d+)_\d\d.tif'
    regex = re.compile(regex)
    match = regex.match(filename)
    if match is not None:
        return int(match.group(1))
    else:
        return None
    
def field_number(filename):
    regex = r'.*RBC\d+_(\d\d).tif'
    regex = re.compile(regex)
    match = regex.match(filename)
    if match is not None:
        return int(match.group(1))
    else:
        return None
    
data['cell number'] = data['filename'].apply(cell_number)
data['field number'] = data['filename'].apply(field_number)

2. Cleaning up the data

Next, we filter the branches by using the shape index. We have used a very simple method to extract skeletons (see Getting started), which does an acceptable job but creates a lot of false branches. Since the goal of Skan is to analyse skeletons, rather than generate them, we attempt to filter the branches, and measure only those that look like ridges according to the shape index.

ridges = ((data['mean-shape-index'] < 0.625) &
          (data['mean-shape-index'] > 0.125))

For the same reason, we only look at junction-to-junction branches, which are more accurately identified by our method than junction-to-endpoint branches.

j2j = data['branch-type'] == 2
datar = data.loc[ridges & j2j].copy()

Finally, we make a new column of measurements in a more natural scale for our purpose.

datar['branch distance (nm)'] = datar['branch-distance'] * 1e9

3. Making the figure

%matplotlib inline
%config InlineBackend.figure_format='retina'

import numpy as np
import imageio as iio
from skimage import morphology
import matplotlib.pyplot as plt
import seaborn as sns

from skan.pre import threshold

fig, axes = plt.subplots(2, 2)
ax = axes.ravel()

# PANEL A
# display an arbitrary image
crop = (slice(20, -20),) * 2
image_raw = iio.v2.imread('schizonts/schizont4_UninfRBC7_06.tif',
                          format='fei')
image = image_raw[crop]
ax[0].imshow(image, cmap='gray')
ax[0].set_axis_off()

# add a 300nm scale bar
height, width = image.shape
scalenm = image.meta['Scan']['PixelHeight'] * 10**9
ax[0].plot((1096, 1096 + 300 / scalenm), (940, 940),
           c='k', lw=2);

# PANEL B
# Next, show the smoothed binary image and corresponding skeleton
radius = int(np.ceil(50/scalenm))
sigma = radius * 0.1
thresholded = threshold(image, sigma=sigma,
                        radius=radius, offset=0.075,
                        smooth_method='gaussian')
viz = np.zeros(image.shape + (3,), dtype=float)
viz[thresholded] = [1, 1, 1]
skeleton = morphology.skeletonize(thresholded)
fat_skeleton = morphology.binary_dilation(skeleton)
viz[fat_skeleton] = [1, 0, 0]
ax[1].imshow(viz)
ax[1].set_axis_off()
ax[1].plot((1096, 1096 + 300 / scalenm), (940, 940),
           c='g', lw=2)

# PANEL C
# Add a panel with a histogram of all branch lengths by infection status
_, bins = np.histogram(datar['branch distance (nm)'], bins='auto')
for inf, df in (datar.sort_values(by='infection', ascending=False)
                .groupby('infection', sort=False)):
    ax[2].hist(df['branch distance (nm)'], bins=bins,
               density=True, alpha=0.5, label=inf)

ax[2].legend()
ax[2].set_xlabel('branch distance (nm)')
ax[2].set_ylabel('density')

# PANEL D
# Finally, a panel grouping the data by cell, showing the difference
# between infected and uninfected cells
cellmeans = (datar.groupby(['infection', 'cell number'])
                  .mean().reset_index())
sns.stripplot(x='infection', y='branch distance (nm)', data=cellmeans,
              jitter=True, order=('normal', 'infected'), ax=ax[3])
              
ax[3].set_xlabel('infection status')
ax[3].set_ylabel('mean branch distance\nby cell (nm)')

# Use matplotlib's automatic layout algorithm
fig.tight_layout()

plt.show()

---------------------------------------------------------------------------
NotImplementedError                       Traceback (most recent call last)
File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/groupby/groupby.py:1490, in GroupBy._cython_agg_general.<locals>.array_func(values)
   1489 try:
-> 1490     result = self.grouper._cython_operation(
   1491         "aggregate",
   1492         values,
   1493         how,
   1494         axis=data.ndim - 1,
   1495         min_count=min_count,
   1496         **kwargs,
   1497     )
   1498 except NotImplementedError:
   1499     # generally if we have numeric_only=False
   1500     # and non-applicable functions
   1501     # try to python agg
   1502     # TODO: shouldn't min_count matter?

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/groupby/ops.py:959, in BaseGrouper._cython_operation(self, kind, values, how, axis, min_count, **kwargs)
    958 ngroups = self.ngroups
--> 959 return cy_op.cython_operation(
    960     values=values,
    961     axis=axis,
    962     min_count=min_count,
    963     comp_ids=ids,
    964     ngroups=ngroups,
    965     **kwargs,
    966 )

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/groupby/ops.py:657, in WrappedCythonOp.cython_operation(self, values, axis, min_count, comp_ids, ngroups, **kwargs)
    649     return self._ea_wrap_cython_operation(
    650         values,
    651         min_count=min_count,
   (...)
    654         **kwargs,
    655     )
--> 657 return self._cython_op_ndim_compat(
    658     values,
    659     min_count=min_count,
    660     ngroups=ngroups,
    661     comp_ids=comp_ids,
    662     mask=None,
    663     **kwargs,
    664 )

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/groupby/ops.py:497, in WrappedCythonOp._cython_op_ndim_compat(self, values, min_count, ngroups, comp_ids, mask, result_mask, **kwargs)
    495     return res.T
--> 497 return self._call_cython_op(
    498     values,
    499     min_count=min_count,
    500     ngroups=ngroups,
    501     comp_ids=comp_ids,
    502     mask=mask,
    503     result_mask=result_mask,
    504     **kwargs,
    505 )

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/groupby/ops.py:541, in WrappedCythonOp._call_cython_op(self, values, min_count, ngroups, comp_ids, mask, result_mask, **kwargs)
    540 out_shape = self._get_output_shape(ngroups, values)
--> 541 func = self._get_cython_function(self.kind, self.how, values.dtype, is_numeric)
    542 values = self._get_cython_vals(values)

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/groupby/ops.py:173, in WrappedCythonOp._get_cython_function(cls, kind, how, dtype, is_numeric)
    171 if "object" not in f.__signatures__:
    172     # raise NotImplementedError here rather than TypeError later
--> 173     raise NotImplementedError(
    174         f"function is not implemented for this dtype: "
    175         f"[how->{how},dtype->{dtype_str}]"
    176     )
    177 return f

NotImplementedError: function is not implemented for this dtype: [how->mean,dtype->object]

During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/nanops.py:1692, in _ensure_numeric(x)
   1691 try:
-> 1692     x = float(x)
   1693 except (TypeError, ValueError):
   1694     # e.g. "1+1j" or "foo"

ValueError: could not convert string to float: 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During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/nanops.py:1696, in _ensure_numeric(x)
   1695 try:
-> 1696     x = complex(x)
   1697 except ValueError as err:
   1698     # e.g. "foo"

ValueError: could not convert string to complex: 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The above exception was the direct cause of the following exception:

TypeError                                 Traceback (most recent call last)
Cell In[10], line 52
     46 ax[2].set_ylabel('density')
     48 # PANEL D
     49 # Finally, a panel grouping the data by cell, showing the difference
     50 # between infected and uninfected cells
     51 cellmeans = (datar.groupby(['infection', 'cell number'])
---> 52                   .mean().reset_index())
     53 sns.stripplot(x='infection', y='branch distance (nm)', data=cellmeans,
     54               jitter=True, order=('normal', 'infected'), ax=ax[3])
     56 ax[3].set_xlabel('infection status')

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/groupby/groupby.py:1855, in GroupBy.mean(self, numeric_only, engine, engine_kwargs)
   1853     return self._numba_agg_general(sliding_mean, engine_kwargs)
   1854 else:
-> 1855     result = self._cython_agg_general(
   1856         "mean",
   1857         alt=lambda x: Series(x).mean(numeric_only=numeric_only),
   1858         numeric_only=numeric_only,
   1859     )
   1860     return result.__finalize__(self.obj, method="groupby")

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/groupby/groupby.py:1507, in GroupBy._cython_agg_general(self, how, alt, numeric_only, min_count, **kwargs)
   1503         result = self._agg_py_fallback(values, ndim=data.ndim, alt=alt)
   1505     return result
-> 1507 new_mgr = data.grouped_reduce(array_func)
   1508 res = self._wrap_agged_manager(new_mgr)
   1509 out = self._wrap_aggregated_output(res)

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/internals/managers.py:1503, in BlockManager.grouped_reduce(self, func)
   1499 if blk.is_object:
   1500     # split on object-dtype blocks bc some columns may raise
   1501     #  while others do not.
   1502     for sb in blk._split():
-> 1503         applied = sb.apply(func)
   1504         result_blocks = extend_blocks(applied, result_blocks)
   1505 else:

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/internals/blocks.py:329, in Block.apply(self, func, **kwargs)
    323 @final
    324 def apply(self, func, **kwargs) -> list[Block]:
    325     """
    326     apply the function to my values; return a block if we are not
    327     one
    328     """
--> 329     result = func(self.values, **kwargs)
    331     return self._split_op_result(result)

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/groupby/groupby.py:1503, in GroupBy._cython_agg_general.<locals>.array_func(values)
   1490     result = self.grouper._cython_operation(
   1491         "aggregate",
   1492         values,
   (...)
   1496         **kwargs,
   1497     )
   1498 except NotImplementedError:
   1499     # generally if we have numeric_only=False
   1500     # and non-applicable functions
   1501     # try to python agg
   1502     # TODO: shouldn't min_count matter?
-> 1503     result = self._agg_py_fallback(values, ndim=data.ndim, alt=alt)
   1505 return result

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/groupby/groupby.py:1457, in GroupBy._agg_py_fallback(self, values, ndim, alt)
   1452     ser = df.iloc[:, 0]
   1454 # We do not get here with UDFs, so we know that our dtype
   1455 #  should always be preserved by the implemented aggregations
   1456 # TODO: Is this exactly right; see WrappedCythonOp get_result_dtype?
-> 1457 res_values = self.grouper.agg_series(ser, alt, preserve_dtype=True)
   1459 if isinstance(values, Categorical):
   1460     # Because we only get here with known dtype-preserving
   1461     #  reductions, we cast back to Categorical.
   1462     # TODO: if we ever get "rank" working, exclude it here.
   1463     res_values = type(values)._from_sequence(res_values, dtype=values.dtype)

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/groupby/ops.py:994, in BaseGrouper.agg_series(self, obj, func, preserve_dtype)
    987 if len(obj) > 0 and not isinstance(obj._values, np.ndarray):
    988     # we can preserve a little bit more aggressively with EA dtype
    989     #  because maybe_cast_pointwise_result will do a try/except
    990     #  with _from_sequence.  NB we are assuming here that _from_sequence
    991     #  is sufficiently strict that it casts appropriately.
    992     preserve_dtype = True
--> 994 result = self._aggregate_series_pure_python(obj, func)
    996 npvalues = lib.maybe_convert_objects(result, try_float=False)
    997 if preserve_dtype:

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/groupby/ops.py:1015, in BaseGrouper._aggregate_series_pure_python(self, obj, func)
   1012 splitter = self._get_splitter(obj, axis=0)
   1014 for i, group in enumerate(splitter):
-> 1015     res = func(group)
   1016     res = libreduction.extract_result(res)
   1018     if not initialized:
   1019         # We only do this validation on the first iteration

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/groupby/groupby.py:1857, in GroupBy.mean.<locals>.<lambda>(x)
   1853     return self._numba_agg_general(sliding_mean, engine_kwargs)
   1854 else:
   1855     result = self._cython_agg_general(
   1856         "mean",
-> 1857         alt=lambda x: Series(x).mean(numeric_only=numeric_only),
   1858         numeric_only=numeric_only,
   1859     )
   1860     return result.__finalize__(self.obj, method="groupby")

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/generic.py:11556, in NDFrame._add_numeric_operations.<locals>.mean(self, axis, skipna, numeric_only, **kwargs)
  11539 @doc(
  11540     _num_doc,
  11541     desc="Return the mean of the values over the requested axis.",
   (...)
  11554     **kwargs,
  11555 ):
> 11556     return NDFrame.mean(self, axis, skipna, numeric_only, **kwargs)

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/generic.py:11201, in NDFrame.mean(self, axis, skipna, numeric_only, **kwargs)
  11194 def mean(
  11195     self,
  11196     axis: Axis | None = 0,
   (...)
  11199     **kwargs,
  11200 ) -> Series | float:
> 11201     return self._stat_function(
  11202         "mean", nanops.nanmean, axis, skipna, numeric_only, **kwargs
  11203     )

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/generic.py:11158, in NDFrame._stat_function(self, name, func, axis, skipna, numeric_only, **kwargs)
  11154     nv.validate_stat_func((), kwargs, fname=name)
  11156 validate_bool_kwarg(skipna, "skipna", none_allowed=False)
> 11158 return self._reduce(
  11159     func, name=name, axis=axis, skipna=skipna, numeric_only=numeric_only
  11160 )

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/series.py:4670, in Series._reduce(self, op, name, axis, skipna, numeric_only, filter_type, **kwds)
   4665     raise TypeError(
   4666         f"Series.{name} does not allow {kwd_name}={numeric_only} "
   4667         "with non-numeric dtypes."
   4668     )
   4669 with np.errstate(all="ignore"):
-> 4670     return op(delegate, skipna=skipna, **kwds)

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/nanops.py:96, in disallow.__call__.<locals>._f(*args, **kwargs)
     94 try:
     95     with np.errstate(invalid="ignore"):
---> 96         return f(*args, **kwargs)
     97 except ValueError as e:
     98     # we want to transform an object array
     99     # ValueError message to the more typical TypeError
    100     # e.g. this is normally a disallowed function on
    101     # object arrays that contain strings
    102     if is_object_dtype(args[0]):

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/nanops.py:158, in bottleneck_switch.__call__.<locals>.f(values, axis, skipna, **kwds)
    156         result = alt(values, axis=axis, skipna=skipna, **kwds)
    157 else:
--> 158     result = alt(values, axis=axis, skipna=skipna, **kwds)
    160 return result

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/nanops.py:421, in _datetimelike_compat.<locals>.new_func(values, axis, skipna, mask, **kwargs)
    418 if datetimelike and mask is None:
    419     mask = isna(values)
--> 421 result = func(values, axis=axis, skipna=skipna, mask=mask, **kwargs)
    423 if datetimelike:
    424     result = _wrap_results(result, orig_values.dtype, fill_value=iNaT)

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/nanops.py:727, in nanmean(values, axis, skipna, mask)
    724     dtype_count = dtype
    726 count = _get_counts(values.shape, mask, axis, dtype=dtype_count)
--> 727 the_sum = _ensure_numeric(values.sum(axis, dtype=dtype_sum))
    729 if axis is not None and getattr(the_sum, "ndim", False):
    730     count = cast(np.ndarray, count)

File /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/pandas/core/nanops.py:1699, in _ensure_numeric(x)
   1696             x = complex(x)
   1697         except ValueError as err:
   1698             # e.g. "foo"
-> 1699             raise TypeError(f"Could not convert {x} to numeric") from err
   1700 return x

TypeError: Could not convert 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Sholl analysis in Skan