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Multi-scale directional
filtering based
method for Follicular
Lymphoma grading
ALİCAN BOZKURT, A. ENIS CETIN
MUSCLE WORKSHOP, ANTALYA
03.10.2013
Follicular Lymphoma
grading
• Follicular Lymphoma (FL)
•

Presence of a follicular or
nodular pattern of growth
presented by follicle center B
cells
• centrocytes and
centroblasts.

Grade 1 (0-5)
Grade 2 (6-15)

Grade 3 (>15)

2
Follicular Lymphoma
grading

Grade 1

Grade 2

Grade 3

3
Follicular Lymphoma
grading
• Pioneer work by Sertel et al:
• mimicked the manual approach of pathologists, i.e., identifying the number
of centroblasts in the sample. Based on this, a decision on the grade of the
sample can be made.
• Accuracy for CB detection was about 80%.

Sertel, Olcay, et al. "Histopathological image analysis using model-based intermediate representations and color texture:
Follicular lymphoma grading." Journal of Signal Processing Systems 55.1-3 (2009): 169-183.

4
Follicular Lymphoma
grading
• Improvement by Suhre
• Hp and Ep denote the projections on the H and E vectors proposed
by Cosatto et al. (2008) to model Hematoxylin and Eosin (H&E)
staining.
• Grades (1,2) and 3 can be distinguished by comparing the
histograms via Kullback-Leibler (KL) divergence.
• For differentiating grades 1 and 2, we choose a Bayesian classifier.
(DCT of the eigenvalue histograms) The underlying PDF is assumed
to be sparse, therefore only q coefficients are used.

Grade 1

Grade 2

Grade 3

98.89

98.89

100

5
Follicular Lymphoma
grading
• Our Work
•
•
•
•

Approaches the problem as texture recognition program
Based on a novel multi-scale feature extraction method
LDA
SVM

6
Directional filtering
•Main idea: rotating a 1D filter along desired orientation
•Easy for θ=k x 45°, k=0,1,2,…
•Not easy for θ≠k x 45°
• Bilinear/cubic interpolation
• Our method: coefficients proportional to length of line segments enclosed
by pixels
• Also used in CT

Herman, Gabor T. "Image reconstruction from projections." Image Reconstruction from Projections: Implementation and Applications 1 (1979).

7
8
Directional filtering

9
Directional Filtering

10
Directional filtering

11
12
Directional Filtering

13
Feature extraction
Step 0

• Input Image

14
Feature extraction
• Input Image
Step 0

Step 1

• Convert Image
to gray level

15
Feature extraction
Step 0

μ1 :
σ1 :

0,082091

0,084891

0,060045

0,080689

0,085836

0,060873

0,14791

0,15201

0,11201

0,14617

0,15402

0,11424

50

50

50

50

100

100

100

100

100

150

150

150

150

150

150

200

200

200

200

200

200

250

250

250

250

250

250

300

300

50

100

300

μ2:
σ2:

300
50

100

150

200

250

300

350

400

450

500

300

300

50
50

100

150

200

250

300

350

400

450

500

50

100

150

200

250

300

350

400

450

100

150

200

250

300

350

400

450

500

500

50

50

100

150

200

250

300

350

400

450

500

50

100

150

200

250

300

350

400

450

0,22597

0,24064

0,11976

0,23731

0,24072

0,36203

0,35692

0,17401

0,37765

0,34842

500

0,12753

Step 2

• Convert Image
to gray level

• Extract
Features

0,19024

20

20

40

40

60

60

60

60

60

60

40

40

40

40

20

20

20

20

80

80

80

80
100

100

100

100

100
120

120

120

120

80

80
1 00
1 20

140

1 60
50

10 0

150

200

250

140

160
50

100

150

200

250

100

150

2 00

140

160
50

50

120

140

160

140

160

1 40

μ3:
σ3:

Step 1

• Input Image

100

150

200

250

250

160

50

100

150

200

25 0

50

100

150

200

250

0,49943 0,54883

0,35954

0,55623

0,56736

0,30949

0,6949

0,46078

0,72141

0,68851

0,39779

0,65361

Φ = [μ1 σ1 μ2 σ2 μ3 σ3] (1x36 feature vector)
16
Classification
[
[

[

θ1
θ2
.
.
.
θN
features

]
]

PCA

Test

10fold
CV
]

LDA

Training

SVM
Train
Par
am
ete
r
sea
rch
for
C
an
dγ

Model

SVM
Classify

Mean
Accuracy

17
Dataset
 Same dataset used by Suhre
 90 images per grade

Grade 1

Grade 2

Grade 3
18
Background

19
Results
Follicular Lymphoma
•Max: 100.00 (Dir. Fil.)
•SoA: 99.26

[20] A. Suhre, Novel Methods for Microscopic Image Processing,
Analysis, Classification and Compression. PhD thesis, Bilkent
University, 2013.

20
Results
6
Grade 1
Grade 2
Grade 3

4

Feature 2

2

0

-2

-4

-6
-10

-8

-6

-4

-2
Feature 1

0

2

4

6

21
Background

22
Results

23
Conclusion
•New directional filter construction and multiscale filtering framework
• Computationally efficient (2x faster than the closest competitor)

•Follicular Lymphoma Grading as an application of the framework
• Mean and standard deviation of directional filter outputs as features
• LDA as feature reduction (to 2D)
• SVM as classifier
• Outperformed state of art

24
Thank You!

25

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Multi Scale Directional Filtering Based Method for Follicular Lymphoma Grading

  • 1. Multi-scale directional filtering based method for Follicular Lymphoma grading ALİCAN BOZKURT, A. ENIS CETIN MUSCLE WORKSHOP, ANTALYA 03.10.2013
  • 2. Follicular Lymphoma grading • Follicular Lymphoma (FL) • Presence of a follicular or nodular pattern of growth presented by follicle center B cells • centrocytes and centroblasts. Grade 1 (0-5) Grade 2 (6-15) Grade 3 (>15) 2
  • 4. Follicular Lymphoma grading • Pioneer work by Sertel et al: • mimicked the manual approach of pathologists, i.e., identifying the number of centroblasts in the sample. Based on this, a decision on the grade of the sample can be made. • Accuracy for CB detection was about 80%. Sertel, Olcay, et al. "Histopathological image analysis using model-based intermediate representations and color texture: Follicular lymphoma grading." Journal of Signal Processing Systems 55.1-3 (2009): 169-183. 4
  • 5. Follicular Lymphoma grading • Improvement by Suhre • Hp and Ep denote the projections on the H and E vectors proposed by Cosatto et al. (2008) to model Hematoxylin and Eosin (H&E) staining. • Grades (1,2) and 3 can be distinguished by comparing the histograms via Kullback-Leibler (KL) divergence. • For differentiating grades 1 and 2, we choose a Bayesian classifier. (DCT of the eigenvalue histograms) The underlying PDF is assumed to be sparse, therefore only q coefficients are used. Grade 1 Grade 2 Grade 3 98.89 98.89 100 5
  • 6. Follicular Lymphoma grading • Our Work • • • • Approaches the problem as texture recognition program Based on a novel multi-scale feature extraction method LDA SVM 6
  • 7. Directional filtering •Main idea: rotating a 1D filter along desired orientation •Easy for θ=k x 45°, k=0,1,2,… •Not easy for θ≠k x 45° • Bilinear/cubic interpolation • Our method: coefficients proportional to length of line segments enclosed by pixels • Also used in CT Herman, Gabor T. "Image reconstruction from projections." Image Reconstruction from Projections: Implementation and Applications 1 (1979). 7
  • 8. 8
  • 12. 12
  • 15. Feature extraction • Input Image Step 0 Step 1 • Convert Image to gray level 15
  • 16. Feature extraction Step 0 μ1 : σ1 : 0,082091 0,084891 0,060045 0,080689 0,085836 0,060873 0,14791 0,15201 0,11201 0,14617 0,15402 0,11424 50 50 50 50 100 100 100 100 100 150 150 150 150 150 150 200 200 200 200 200 200 250 250 250 250 250 250 300 300 50 100 300 μ2: σ2: 300 50 100 150 200 250 300 350 400 450 500 300 300 50 50 100 150 200 250 300 350 400 450 500 50 100 150 200 250 300 350 400 450 100 150 200 250 300 350 400 450 500 500 50 50 100 150 200 250 300 350 400 450 500 50 100 150 200 250 300 350 400 450 0,22597 0,24064 0,11976 0,23731 0,24072 0,36203 0,35692 0,17401 0,37765 0,34842 500 0,12753 Step 2 • Convert Image to gray level • Extract Features 0,19024 20 20 40 40 60 60 60 60 60 60 40 40 40 40 20 20 20 20 80 80 80 80 100 100 100 100 100 120 120 120 120 80 80 1 00 1 20 140 1 60 50 10 0 150 200 250 140 160 50 100 150 200 250 100 150 2 00 140 160 50 50 120 140 160 140 160 1 40 μ3: σ3: Step 1 • Input Image 100 150 200 250 250 160 50 100 150 200 25 0 50 100 150 200 250 0,49943 0,54883 0,35954 0,55623 0,56736 0,30949 0,6949 0,46078 0,72141 0,68851 0,39779 0,65361 Φ = [μ1 σ1 μ2 σ2 μ3 σ3] (1x36 feature vector) 16
  • 18. Dataset  Same dataset used by Suhre  90 images per grade Grade 1 Grade 2 Grade 3 18
  • 20. Results Follicular Lymphoma •Max: 100.00 (Dir. Fil.) •SoA: 99.26 [20] A. Suhre, Novel Methods for Microscopic Image Processing, Analysis, Classification and Compression. PhD thesis, Bilkent University, 2013. 20
  • 21. Results 6 Grade 1 Grade 2 Grade 3 4 Feature 2 2 0 -2 -4 -6 -10 -8 -6 -4 -2 Feature 1 0 2 4 6 21
  • 24. Conclusion •New directional filter construction and multiscale filtering framework • Computationally efficient (2x faster than the closest competitor) •Follicular Lymphoma Grading as an application of the framework • Mean and standard deviation of directional filter outputs as features • LDA as feature reduction (to 2D) • SVM as classifier • Outperformed state of art 24

Editor's Notes

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