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| PMC full text: | Phys Med Biol. Author manuscript; available in PMC 2023 Nov 9. Published in final edited form as: Phys Med Biol. 2022 Nov 9; 67(22): 10.1088/1361-6560/ac8fde. Published online 2022 Nov 9. doi: 10.1088/1361-6560/ac8fde |
Table 2.
A list of image analysis algorithms available on the DPLab platform.
| Title | Input Data Type | Output Data Type | Language | Description |
|---|---|---|---|---|
| Cell Seed Detection (Conventional methods) | 2D Images | Points | MATLAB | Detection of cells with information from spatial connectivity, edge map, and a voting mechanism with a local shape-based intensity analysis; Tested on brain tissues in H&E stain. |
| Cell Seed Detection (Deep Learning) | 2D Images | Points | Python, C, C++ | Detection of cells using Convolutional Neural Network (CNN) with interactive learning; Tested on brain tissues in H&E stain. |
| Cell Segmentation (Hysteresis Thresholding) | 2D Images | Polygonal ROIs | MATLAB | Segmentation and division of cells with Hysteresis analysis and watershed method; Tested on brain tissues in H&E stain. |
| IHC Positive Pixel Counting | 2D Images | Polygonal ROIs, Percentages | MATLAB | Identification of pixels with strong, intermediate, and weak stain intensity; Tested on liver tissues with CD34 IHC biomarker. |
| Steatosis Segmentation and Segregation (Conventional methods) | 2D Images | Polygonal ROIs | MATLAB | Segmentation and segregation of liver steatosis for quantification; Tested on liver tissues in Masson Trichrome stain. |
| Steatosis Segmentation and Segregation (Deep Learning based) | 2D Images | Polygonal ROIs | Python | Segmentation and segregation of liver steatosis for quantification; Tested on liver tissues in Masson Trichrome stain. |
| Dynamic Serial Slide Registration | 2D Serial WSIs | 3D Image Volume | MATLAB | Dynamic registration of user-specified regions from whole-slide serial pathology image sequence with multi-stage and multi-resolution mapping and aggregation methods; Tested on brain, liver and breast tissues in H&E, IHC, and Masson Trichrome stain. |
| DAPI Nuclei Segmentation | 3D MultiChannel Image | 2D Image of Components | Python | DAPI signal based nuclei segmentation by deep learning with Imaging Mass Cytometry data; Tested on imaging mass cytometry images of breast tissues. |
| Fibrosis (Conventional methods) | 2D Images | Polygonal ROIs | MATLAB | Identifications of liver fibrosis regions with contours; Tested on liver tissues in Masson Trichrome stain. |
| Fibrosis (Deep Learning based) | 2D Images | Polygonal ROIs | Python | Identifications of liver fibrosis regions with contours; Tested on liver tissues in Masson Trichrome stain. |
| Color Deconvolution | 2D Images | 2D Images | Python | Color deconvolution/unmixing for HE, IHC or other customized stain images; Tested on brain and liver tissues in H&E and IHC. |
| Color normalization | 2D Images | 2D Images | Python | Normalization of color with HE, IHC, or other customized stain images; Tested on brain and liver tissues in H&E and IHC. |
| White Area Segmentation | 2D Images | 2D Images | Python | Segmentation of white areas within tissue images; Tested on brain and liver tissues in H&E and IHC. |
| Extract region of interest from WSIs | 2D Images | 2D Images | Python | Annotation, extraction, and download of regions of interest from a WSI; Tested on brain and liver tissues in H&E and IHC. |