Table 1.
A summary of select useful functions in image processing in Python and R
| Program | Package/library | Function | Brief description |
|---|---|---|---|
| Python | Py_wsi | Sample_and_store_patches | Sample tiles (patches) from a WSI |
| OpenCV | Dilate, erosion, etc. | ||
| scikit-image | Rgb2hed | Color deconvolution for WSIs | |
| Match_histograms | Histogram matching for color normalization | ||
| Threshold_otsu | Otsu thresholding | ||
| Scipy | Center_of_mass() | Calculate object location | |
| Find_objects() | Find objects in an array | ||
| Label() | Label features in an array | ||
| pgmagick | Image conversions | ||
| R | EBImage | computeFeatures | Calculate sizes of objects |
| removeObjects | Remove objects | ||
| Filter2D | Apply a filter to an image | ||
| Dilate, erosion, etc. | Morphological operations | ||
| Bwlabel() | Label objects | ||
| Otsu() | Otsu thresholding | ||
| Tiff, jpeg, png | Read/write | Read and write images of different file types | |
| Magick | Image conversions | ||
| Reticulate | Compile Python code in R | ||
| Windows/Linux | ImageMagick | Command-line package for image manipulation |