Object classification with APOC and SimpleITK-based features#

Classifying objects can involve extracting custom features. We simulate this scenario by using SimpleITK-based features as available in napari-simpleitk-image-processing and train an APOC table-row-classifier.

See also

from skimage.io import imread
from pyclesperanto_prototype import imshow, replace_intensities
from skimage.filters import threshold_otsu
from skimage.measure import label, regionprops
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from napari_simpleitk_image_processing import label_statistics
import apoc

Our starting point are an image, a label image and some ground truth annotation. The annotation is also a label image where the user was just drawing lines with different intensity (class) through small objects, large objects and elongated objects.

# load and label data
image = imread('../../data/blobs.tif')
labels = label(image > threshold_otsu(image))
annotation = imread('../../data/label_annotation.tif')

# visualize
fig, ax = plt.subplots(1,3, figsize=(15,15))
imshow(image, plot=ax[0])
imshow(labels, plot=ax[1], labels=True)
imshow(image, plot=ax[2], continue_drawing=True)
imshow(annotation, plot=ax[2], alpha=0.7, labels=True)
../_images/apoc_simpleitk_object_classification_3_0.png

Feature extraction#

The first step to classify objects according to their properties is feature extraction. We will use the scriptable napari plugin napari-simpleitk-image-processing for that.

statistics = label_statistics(image, labels, None, True, True, True, True, True, True)

statistics_table = pd.DataFrame(statistics)
statistics_table
label maximum mean median minimum sigma sum variance bbox_0 bbox_1 ... number_of_pixels_on_border perimeter perimeter_on_border perimeter_on_border_ratio principal_axes0 principal_axes1 principal_axes2 principal_axes3 principal_moments0 principal_moments1
0 1 232.0 190.854503 200.0 128.0 30.304925 82640.0 918.388504 10 0 ... 17 89.196525 17.0 0.190590 0.902586 0.430509 -0.430509 0.902586 17.680049 76.376232
1 2 224.0 179.286486 184.0 128.0 21.883314 33168.0 478.879436 53 0 ... 21 53.456120 21.0 0.392846 -0.051890 -0.998653 0.998653 -0.051890 8.708186 27.723954
2 3 248.0 205.617021 208.0 128.0 29.380812 135296.0 863.232099 95 0 ... 23 93.409370 23.0 0.246228 0.988608 0.150515 -0.150515 0.988608 49.978765 57.049896
3 4 248.0 217.327189 232.0 128.0 36.061134 94320.0 1300.405402 144 0 ... 19 75.558902 19.0 0.251459 0.870813 0.491615 -0.491615 0.870813 33.246984 37.624111
4 5 248.0 212.142558 224.0 128.0 29.904270 101192.0 894.265349 237 0 ... 39 82.127941 40.0 0.487045 0.998987 0.045005 -0.045005 0.998987 24.584386 60.694273
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
59 60 128.0 128.000000 128.0 128.0 0.000000 128.0 0.000000 110 246 ... 0 2.681517 0.0 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000
60 61 248.0 183.407407 176.0 128.0 34.682048 14856.0 1202.844444 170 248 ... 19 41.294008 19.0 0.460115 -0.005203 -0.999986 0.999986 -0.005203 2.190911 21.525901
61 62 216.0 181.511111 184.0 128.0 25.599001 16336.0 655.308864 116 249 ... 23 48.093086 23.0 0.478239 -0.023708 -0.999719 0.999719 -0.023708 1.801689 31.523372
62 63 248.0 188.377358 184.0 128.0 38.799398 9984.0 1505.393324 227 249 ... 16 34.264893 16.0 0.466950 0.004852 -0.999988 0.999988 0.004852 1.603845 13.711214
63 64 224.0 172.897959 176.0 128.0 28.743293 8472.0 826.176871 66 250 ... 17 35.375614 17.0 0.480557 0.022491 -0.999747 0.999747 0.022491 0.923304 18.334505

64 rows × 33 columns

statistics_table.columns
Index(['label', 'maximum', 'mean', 'median', 'minimum', 'sigma', 'sum',
       'variance', 'bbox_0', 'bbox_1', 'bbox_2', 'bbox_3', 'centroid_0',
       'centroid_1', 'elongation', 'feret_diameter', 'flatness', 'roundness',
       'equivalent_ellipsoid_diameter_0', 'equivalent_ellipsoid_diameter_1',
       'equivalent_spherical_perimeter', 'equivalent_spherical_radius',
       'number_of_pixels', 'number_of_pixels_on_border', 'perimeter',
       'perimeter_on_border', 'perimeter_on_border_ratio', 'principal_axes0',
       'principal_axes1', 'principal_axes2', 'principal_axes3',
       'principal_moments0', 'principal_moments1'],
      dtype='object')
table = statistics_table[['number_of_pixels','elongation']]
table
number_of_pixels elongation
0 433 2.078439
1 185 1.784283
2 658 1.068402
3 434 1.063793
4 477 1.571246
... ... ...
59 1 0.000000
60 81 3.134500
61 90 4.182889
62 53 2.923862
63 49 4.456175

64 rows × 2 columns

We also read out the maximum intensity of every labeled object from the ground truth annotation. These values will serve to train the classifier. Entries of 0 correspond to objects that have not been annotated.

annotation_stats = regionprops(labels, intensity_image=annotation)

annotated_classes = np.asarray([s.max_intensity for s in annotation_stats])
print(annotated_classes)
[0. 0. 2. 0. 0. 0. 2. 0. 0. 0. 3. 0. 0. 0. 3. 0. 0. 3. 0. 0. 0. 3. 0. 0.
 0. 0. 1. 0. 0. 0. 1. 2. 1. 0. 0. 2. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.]

Classifier Training#

Next, we can train the Random Forest Classifer. It needs tablue training data and a ground truth vector.

classifier_filename = 'table_row_classifier.cl'

classifier = apoc.TableRowClassifier(opencl_filename=classifier_filename, max_depth=2, num_ensembles=10)
classifier.train(table, annotated_classes)

Prediction#

To apply a classifier to the whole dataset, or any other dataset, we need to make sure that the data is in the same format. This is trivial in case we analyse the same dataset we trained on.

predicted_classes = classifier.predict(table)
predicted_classes
array([1, 1, 2, 3, 3, 3, 2, 3, 2, 1, 3, 3, 3, 2, 3, 1, 3, 3, 3, 3, 3, 3,
       1, 3, 3, 3, 3, 1, 3, 3, 1, 2, 1, 2, 2, 3, 3, 1, 1, 3, 3, 3, 3, 2,
       3, 2, 3, 2, 1, 3, 1, 3, 3, 1, 3, 3, 3, 3, 1, 2, 1, 1, 1, 1],
      dtype=uint32)

For documentation purposes, we can save the annotated class and the predicted class into the our table. Note: We’re doing this after training, because otherwise e.g. the column

table
number_of_pixels elongation
0 433 2.078439
1 185 1.784283
2 658 1.068402
3 434 1.063793
4 477 1.571246
... ... ...
59 1 0.000000
60 81 3.134500
61 90 4.182889
62 53 2.923862
63 49 4.456175

64 rows × 2 columns

table['annotated_class'] = annotated_classes
table['predicted_class'] = predicted_classes
table
/var/folders/p1/6svzckgd1y5906pfgm71fvmr0000gn/T/ipykernel_4463/2818530951.py:1: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  table['annotated_class'] = annotated_classes
/var/folders/p1/6svzckgd1y5906pfgm71fvmr0000gn/T/ipykernel_4463/2818530951.py:2: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  table['predicted_class'] = predicted_classes
number_of_pixels elongation annotated_class predicted_class
0 433 2.078439 0.0 1
1 185 1.784283 0.0 1
2 658 1.068402 2.0 2
3 434 1.063793 0.0 3
4 477 1.571246 0.0 3
... ... ... ... ...
59 1 0.000000 0.0 2
60 81 3.134500 0.0 1
61 90 4.182889 0.0 1
62 53 2.923862 0.0 1
63 49 4.456175 0.0 1

64 rows × 4 columns

Furthermore, we can use the same vector to use replace_intensities to generate a class_image. The background and objects with NaNs in measurements will have value 0 in that image.

# we add a 0 for the class of background at the beginning
predicted_classes_with_background = [0] + predicted_classes.tolist()
print(predicted_classes_with_background)
[0, 1, 1, 2, 3, 3, 3, 2, 3, 2, 1, 3, 3, 3, 2, 3, 1, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 3, 1, 3, 3, 1, 2, 1, 2, 2, 3, 3, 1, 1, 3, 3, 3, 3, 2, 3, 2, 3, 2, 1, 3, 1, 3, 3, 1, 3, 3, 3, 3, 1, 2, 1, 1, 1, 1]
class_image = replace_intensities(labels, predicted_classes_with_background)
imshow(class_image, colorbar=True, colormap='jet', min_display_intensity=0)
../_images/apoc_simpleitk_object_classification_19_0.png