| Literature DB >> 35242444 |
Keluo Yao1, Xin Jing2, Jerome Cheng2, Ulysses G J Balis2, Liron Pantanowitz2, Madelyn Lew2.
Abstract
BACKGROUND: Originally designed for computerized image analysis, ThinPrep is underutilized in that role outside gynecological cytology. It can be used to address the inter/intra-observer variability in the evaluation of thyroid fine needle aspiration (TFNA) biopsy and help pathologists to gain additional insight into thyroid cytomorphology.Entities:
Keywords: Bethesda; Digital image analysis; Fine needle aspiration; ThinPrep; Thyroid
Year: 2022 PMID: 35242444 PMCID: PMC8864759 DOI: 10.1016/j.jpi.2022.100004
Source DB: PubMed Journal: J Pathol Inform
Figure 1The segmentation and feature extraction of each image (A) starts with background subtraction (B), followed by conversion to 8-bit grayscale image (green channel only) through color deconvolution (C), automatic threshold segmentation, and finally a mask (red) for the nuclear features (D). The extracted nuclei features are further “gated” (high-power only) using size and circularity to separate out individual nuclei from closely grouped clusters.
Details of the predictive models and features performance.
| Magnification1 | High2 | Medium3 | Low4 | Gate5 | Mean/StdDv6 | Feature importance7 | FA value8 | B9 value9 | T-test score10 |
|---|---|---|---|---|---|---|---|---|---|
| Mid-power | Cellularity | N/A | CountI | None | Mean | 0.143 | 268.57 | 164.31 | 0.000 |
| Mid-power | Cellularity | N/A | Total AreaII | None | Mean | 0.104 | 41191.52 | 24885.81 | 0.001 |
| Mid-power | N/A | N/A | AreaIII | None | Mean | 0.060 | 153.44 | 129.37 | 0.122 |
| Mid-power | N/A | N/A | CircIV | None | Mean | 0.083 | 0.90 | 0.90 | 0.832 |
| Mid-power | N/A | N/A | MaxFeretV | None | Mean | 0.067 | 12.84 | 12.27 | 0.248 |
| Mid-power | N/A | N/A | IntDenVI | None | Mean | 0.056 | 25581.13 | 21781.70 | 0.175 |
| Mid-power | N/A | N/A | KurtVII | None | Mean | 0.066 | -1.03 | -1.02 | 0.586 |
| Mid-power | N/A | N/A | MeanVIII | None | Mean | 0.061 | 174.81 | 177.03 | 0.263 |
| Mid-power | N/A | N/A | MedianIX | None | Mean | 0.057 | 176.21 | 178.17 | 0.329 |
| Mid-power | N/A | N/A | MinFeretX | None | Mean | 0.067 | 8.59 | 8.25 | 0.258 |
| Mid-power | N/A | N/A | ModeXI | None | Mean | 0.061 | 177.56 | 179.19 | 0.465 |
| Mid-power | N/A | N/A | PerimXII | None | Mean | 0.062 | 35.12 | 33.14 | 0.180 |
| Mid-power | N/A | N/A | SkewXIII | None | Mean | 0.055 | -0.28 | -0.26 | 0.050 |
| Mid-power | N/A | N/A | SolidityXIV | None | Mean | 0.058 | 0.89 | 0.89 | 0.519 |
| High-power | Architecture | N/A | ARXV | Cluster | StdDv | 0.010 | 0.38 | 0.30 | 0.017 |
| High-power | Architecture | N/A | AR | Cluster | Mean | 0.009 | 1.74 | 1.46 | 0.001 |
| High-power | Architecture | N/A | Area | Cluster | Mean | 0.014 | 5711.59 | 2252.09 | 0.000 |
| High-power | Architecture | N/A | Area | Cluster | StdDv | 0.009 | 4731.23 | 1443.71 | 0.000 |
| High-power | Architecture | N/A | Circ | Cluster | StdDv | 0.014 | 0.11 | 0.07 | 0.000 |
| High-power | Architecture | N/A | Circ | Cluster | Mean | 0.009 | 0.32 | 0.27 | 0.003 |
| High-power | Architecture | N/A | MaxFeret | Cluster | Mean | 0.016 | 98.85 | 67.44 | 0.000 |
| High-power | Architecture | N/A | MaxFeret | Cluster | StdDv | 0.009 | 40.91 | 18.64 | 0.000 |
| High-power | Architecture | N/A | MinFeret | Cluster | Mean | 0.011 | 60.02 | 40.96 | 0.000 |
| High-power | Architecture | N/A | MinFeret | Cluster | StdDv | 0.009 | 25.45 | 11.62 | 0.000 |
| High-power | Architecture | N/A | Perim | Cluster | Mean | 0.015 | 432.76 | 264.52 | 0.000 |
| High-power | Architecture | N/A | Perim | Cluster | StdDv | 0.010 | 274.11 | 108.59 | 0.000 |
| High-power | Architecture | N/A | Round | Cluster | Mean | 0.012 | 0.52 | 0.44 | 0.001 |
| High-power | Architecture | N/A | Round | Cluster | StdDv | 0.008 | 0.11 | 0.09 | 0.004 |
| High-power | Architecture | N/A | Solidity | Cluster | Mean | 0.015 | 0.69 | 0.57 | 0.000 |
| High-power | Architecture | N/A | Solidity | Cluster | StdDv | 0.012 | 0.06 | 0.04 | 0.000 |
| High-power | Cytology | Chromatin | IntDen | Single | StdDv | 0.020 | 17007.18 | 12785.69 | 0.000 |
| High-power | Cytology | Chromatin | IntDen | Cluster | Mean | 0.016 | 478875.76 | 169419.42 | 0.000 |
| High-power | Cytology | Chromatin | IntDen | Single | Mean | 0.016 | 40865.41 | 34437.49 | 0.000 |
| High-power | Cytology | Chromatin | IntDen | Cluster | StdDv | 0.010 | 395319.99 | 139400.12 | 0.004 |
| High-power | Cytology | Chromatin | Kurt | Single | StdDv | 0.013 | 0.47 | 0.43 | 0.121 |
| High-power | Cytology | Chromatin | Kurt | Cluster | Mean | 0.013 | -0.48 | -0.38 | 0.046 |
| High-power | Cytology | Chromatin | Kurt | Single | Mean | 0.012 | -0.51 | -0.46 | 0.079 |
| High-power | Cytology | Chromatin | Kurt | Cluster | StdDv | 0.008 | 0.38 | 0.30 | 0.126 |
| High-power | Cytology | Chromatin | MaxXVI | Single | StdDv | 0.028 | 4.55 | 2.96 | 0.000 |
| High-power | Cytology | Chromatin | Max | Single | Mean | 0.020 | 127.32 | 115.62 | 0.001 |
| High-power | Cytology | Chromatin | Max | Cluster | Mean | 0.015 | 132.70 | 99.76 | 0.000 |
| High-power | Cytology | Chromatin | Max | Cluster | StdDv | 0.008 | 11.49 | 7.99 | 0.010 |
| High-power | Cytology | Chromatin | Mean | Cluster | Mean | 0.018 | 76.34 | 56.04 | 0.000 |
| High-power | Cytology | Chromatin | Mean | Cluster | StdDv | 0.016 | 6.67 | 3.76 | 0.000 |
| High-power | Cytology | Chromatin | Mean | Single | StdDv | 0.014 | 11.75 | 9.78 | 0.000 |
| High-power | Cytology | Chromatin | Mean | Single | Mean | 0.012 | 82.00 | 73.23 | 0.001 |
| High-power | Cytology | Chromatin | MedianXVII | Cluster | StdDv | 0.019 | 8.29 | 4.69 | 0.000 |
| High-power | Cytology | Chromatin | Median | Cluster | Mean | 0.015 | 75.08 | 54.08 | 0.000 |
| High-power | Cytology | Chromatin | Median | Single | StdDv | 0.015 | 14.33 | 11.99 | 0.000 |
| High-power | Cytology | Chromatin | Median | Single | Mean | 0.013 | 78.86 | 69.88 | 0.001 |
| High-power | Cytology | Chromatin | MinXVIII | Single | StdDv | 0.015 | 14.14 | 11.14 | 0.001 |
| High-power | Cytology | Chromatin | Min | Single | Mean | 0.014 | 43.59 | 40.29 | 0.108 |
| High-power | Cytology | Chromatin | Min | Cluster | Mean | 0.012 | 28.39 | 22.31 | 0.001 |
| High-power | Cytology | Chromatin | Min | Cluster | StdDv | 0.009 | 7.88 | 4.86 | 0.000 |
| High-power | Cytology | Chromatin | ModeXIX | Cluster | Mean | 0.019 | 70.14 | 47.87 | 0.000 |
| High-power | Cytology | Chromatin | Mode | Cluster | StdDv | 0.018 | 14.81 | 9.01 | 0.000 |
| High-power | Cytology | Chromatin | Mode | Single | StdDv | 0.014 | 20.49 | 16.81 | 0.000 |
| High-power | Cytology | Chromatin | Mode | Single | Mean | 0.012 | 71.10 | 62.52 | 0.001 |
| High-power | Cytology | Chromatin | RawIntDen | Single | Mean | 0.018 | 40865.41 | 34437.49 | 0.000 |
| High-power | Cytology | Chromatin | RawIntDen | Single | StdDv | 0.016 | 17007.18 | 12785.69 | 0.000 |
| High-power | Cytology | Chromatin | RawIntDen | Cluster | Mean | 0.015 | 478875.76 | 169419.42 | 0.000 |
| High-power | Cytology | Chromatin | RawIntDen | Cluster | StdDv | 0.009 | 395319.99 | 139400.12 | 0.004 |
| High-power | Cytology | Chromatin | Skew | Single | Mean | 0.021 | 0.34 | 0.47 | 0.000 |
| High-power | Cytology | Chromatin | Skew | Cluster | Mean | 0.015 | 0.14 | 0.25 | 0.006 |
| High-power | Cytology | Chromatin | Skew | Single | StdDv | 0.010 | 0.39 | 0.37 | 0.089 |
| High-power | Cytology | Chromatin | Skew | Cluster | StdDv | 0.010 | 0.26 | 0.17 | 0.000 |
| High-power | Cytology | Chromatin | StdDev | Single | Mean | 0.023 | 20.07 | 18.20 | 0.002 |
| High-power | Cytology | Chromatin | StdDev | Single | StdDv | 0.012 | 4.58 | 3.49 | 0.000 |
| High-power | Cytology | Chromatin | StdDev | Cluster | Mean | 0.011 | 21.90 | 16.84 | 0.000 |
| High-power | Cytology | Chromatin | StdDev | Cluster | StdDv | 0.011 | 2.88 | 1.91 | 0.000 |
| High-power | Cytology | Shape | AR | Single | Mean | 0.017 | 1.31 | 1.34 | 0.038 |
| High-power | Cytology | Shape | AR | Single | StdDv | 0.012 | 0.27 | 0.28 | 0.163 |
| High-power | Cytology | Shape | Circ | Single | Mean | 0.022 | 0.73 | 0.76 | 0.004 |
| High-power | Cytology | Shape | Circ | Single | StdDv | 0.012 | 0.10 | 0.09 | 0.405 |
| High-power | Cytology | Shape | MaxFeret | Single | Mean | 0.016 | 29.13 | 29.01 | 0.804 |
| High-power | Cytology | Shape | MaxFeret | Single | StdDv | 0.012 | 6.20 | 5.77 | 0.064 |
| High-power | Cytology | Shape | MinFeret | Single | Mean | 0.016 | 22.33 | 21.77 | 0.127 |
| High-power | Cytology | Shape | MinFeret | Single | StdDv | 0.013 | 4.28 | 3.76 | 0.001 |
| High-power | Cytology | Shape | Perim | Single | Mean | 0.018 | 87.90 | 85.51 | 0.108 |
| High-power | Cytology | Shape | Perim | Single | StdDv | 0.011 | 19.23 | 17.45 | 0.010 |
| High-power | Cytology | Shape | Round | Single | Mean | 0.019 | 0.77 | 0.76 | 0.230 |
| High-power | Cytology | Shape | Round | Single | StdDv | 0.009 | 0.13 | 0.13 | 0.995 |
| High-power | Cytology | Shape | Solidity | Single | Mean | 0.019 | 0.89 | 0.90 | 0.265 |
| High-power | Cytology | Shape | Solidity | Single | StdDv | 0.011 | 0.03 | 0.03 | 0.371 |
| High-power | Cytology | Size | Area | Single | Mean | 0.016 | 482.09 | 461.70 | 0.100 |
| High-power | Cytology | Size | Area | Single | StdDv | 0.011 | 183.26 | 157.58 | 0.000 |
1. The magnification models are consisted of mid-power (100x) and high-power (400x) models. 2. High = high level features; 3. Medium = medium level features; 4. Low = low level features. 5. The “gate” filters follicular cell nuclei into single vs overlapping clusters based on: single nuclei have areas (III) between 100 and 1200 pixels and circ (IV) between 0.5 and 1.0; overlapping clusters have areas (III) between 1200 to infinite pixels and circularity between 0.0 and 1.0. 6. Values collected as mean vs standard deviation. 7. Feature importance dictates contribution (in percentage) of each feature to the predictive accuracy of the model. 8. Average value collected from follicular adenoma images. 9. Average value collected from benign (B9) thyroid images. 10. Student’s P values of each feature based on comparing values from follicular adenoma vs benign thyroid.
Count (I) - Number of separated nuclei, including both single and clustered nuclei; Total area (II) - Total area of the image occupied by nuclei in pixels; each pixel corresponds to an area of 0.064 μM2 for the high-power model and 0.016 μM2 for the mid-power model; Area (III) - Area of region of individual nuclei in square pixels; Circ (IV) - 4 π (Area/Perimeter2); 1.0 is a perfect circle; the value approaches 0 as the shape elongates; MaxFeret (V) - Feret's diameter: Maximum caliper; conversion factor 0.08 μM for high-power model and 0.04 μM for mid-power model; IntDen (VI) - Integrated density: area times mean gray value; Kurt (VII) - Kurtosis: The fourth-order moment about the mean; Mean (VIII) - Average gray value of the pixels in each nucleus/cluster of nuclei; The values range from 0 to 255; Medium (IX) - The median gray value of the pixels in the entire image; MinFeret (X) - Minmum Feret's diameter: minimum caliper; conversion factor 0.08 μM for high-power model and 0.04 μM for mid-power model; Mode (XI) - Most frequently occurring gray value of the pixels in each nucleus/cluster of nuclei; Perim (XII) - The length of the outside boundary of each nucleus/cluster of nuclei; multiple the value by 0.08 to get a measurement in μM for the high-power model and 0.04 for the mid-power model; Skew (XIII) - The third-order moment about the mean; Solidity (XIV) - Area/Convex Area; AR (XV) - Aspect ratio: Major axis/Minor axis; Max (XVI) - Maximum gray values of the pixels in each nucleus/cluster of nuclei; value range from 0 to 255; Median (XVII) - The median value of the pixels in the entire image; values range from 0 to 255; Min (XVIII) - Minimum gray values of the pixels in each nucleus/cluster of nuclei; values range from 0 to 255; Mode (XIX) - Most frequently occurring gray value of the pixels in each nucleus/cluster of nuclei; values range from 0 to 255.
Figure 2The predictive performance evaluation of mid-power (A) and high-power (B) models, high level features (A-1, B-1, B-2), and medium level features (B-3, B-4, B-5) using receiver operating characteristics (ROC) and quantified by area under the curve (AUC); ETC = extra tree classifier; GBC = gradient boost classifier.
| AUC | Area under the curve |
| AUS | Atypia of undetermined significance |
| DIA | Digital image analysis |
| ETC | Extra tree classifier |
| FLUS | Follicular lesion of undetermined significance |
| FNA | Fine needle aspiration |
| GBC | Gradient boost classifier |
| ROC | Receiver operating characteristics |
| SQL | Structured query language |
| TFNA | Thyroid fine needle aspiration |