bjpcjp/scikit-image

scikit-image sandbox

scikit-image

notes

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notebooks

• applications
  • 3D image processing
  • kidney tissue 3D
  • Estimate anisotropy in a 3D microscopy image -
  • coins segmentation
  • colocalization metrics
  • cornea spot inpainting
  • face detection
  • fluorescence
  • haar extraction
  • human mitosis
  • image comparison
  • morphology
  • pixel graphs
  • rank filters
  • solidification
  • text
  • thresholding

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• color_exposure
  • adaptive histogram equalization (AHE)
  • Adapting gray-scale filters to RGB images
  • Histogram Equalization
  • Histogram matching
  • Color separation - immunohistochemical staining
  • Histogram Equalization (local)
  • Contrast adjustments
  • Filtering regional maxima
  • RGB to grayscale
  • RGB to HSV
  • Tinting gray-scale images

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• datasets
  • 3D images
  • various general images
  • scientific images
  • stereo and facial images

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• developers
  • Max trees
  • Background/foreground thresholds

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• edges
  • active contours
  • canny edge detector
  • hough transforms - circular & elliptical
  • contour finding
  • convex hulls
  • edge filters
  • hough transforms - straight lines
  • marching cubes
  • polygon approximation & subdividing
  • random shape generation
  • ridge filters
  • drawing std shapes
  • skeletonizing

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• features_detection
  • Blob detection - 3 alternate algorithms
  • BRIEF binary descriptor
  • CENSURE
  • Corner detection
  • DAISY local image descriptor
  • Fisher vector feature encoding
  • Gabor filter banks for texture classification
  • Gabors / Primary Visual Cortex "Simple Cells" from an Image
  • GLCM Texture Features
  • Haar-like feature descriptor
  • HOG (Histogram of Oriented Gradients)
  • Filling holes and finding peaks
  • Local Binary Pattern for texture classification
  • Local Binary Pattern (multiblock) for texture classification
  • ORB feature detector and binary descriptor
  • Shape Index
  • SIFT feature detector and descriptor extractor
  • Template Matching
  • Sliding window histogram

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• filters
  • family of contour preserving filtering operations in mathematical morphology
  • estimate blur strength
  • butterworth filtering
  • Shift-invariant wavelet denoising
    • ensure PyWavelets is installed
  • Image deconvolution using the Richardson-Lucy algo
  • Image denoising with total variation, bilateral, and wavelet filters
  • Wavelet denoising with VisuShrink & BayesShrink algos
  • Band-pass filtering - Difference of Gaussians
  • Image entropy
  • hysteresis thresholding vs normal thresholding
  • reconstructing lost or deteriorated parts of images and videos
  • calibrating Denoisers Using J-Invariance
  • plot_j_invariant_tutorial
  • Non-local means denoising for preserving textures
  • [plot_phase_unwrap](.ipynb
  • compares 3 mean filters of the rank filter package
  • Deconvolve a noisy image using Wiener and unsupervised Wiener algorithms
  • Removing small objects in grayscale images with a top hat filter
  • linear image sharpening technique
  • Image windowing with FFTs

---

• numpy_operations
  • simple NumPy image operations
  • footprint decomposition
  • footprint generation
  • view as blocks

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• registration
  • identify the relative shift between two similar images containing invalid data
  • Registration using optical flow
  • Using Polar and Log-Polar Transformations
  • Use phase cross-correlation to ID the relative shift between two similar-sized images
  • Assemble images with simple image stitching

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• segmentation
  • Hierarchical Merging of Region Boundary RAGs
  • Chan-Vese segmentation. Used for poorly defined boundries
  • Find regular segments using compact watershed
  • Euler numbers
  • Expanding segmentation labels without overlap
  • Detecting local extrema in an image
  • 'paint bucket'
  • hausdorff_distance
  • Find the intersection of two segments
  • segment an image with image labelling
  • markers for watershed transforms
  • compare segmentations obtained with SLIC and its masked version maskSLIC
  • segmentation metrics: watershed vs Canny vs Morphological geodesic
  • MorphGAC vs MorphACWE for image segmentation
  • Multi-Otsu thresholding
  • Normalized cuts
  • Niblack and Sauvola thresholding
  • Finding local maxima
  • Perimeter estimation - classic vs Crofton estimators
  • Region boundary based RAGs
  • Drawing RAGs
  • Demos merge_nodes function of a RAG
  • Build a RAG, then merge regions which are similar in color
  • RAG merge
  • Random walker segmentation
  • Explore and visualize region properties with pandas
  • Measure properties of labelled image regions
  • rolling-ball algorithm for estimating background intensity
    • NOTE: a portion of this notebook uses the pywt package which isn't currently available?
  • image segmentation - 4 methods
  • Create a binary image from a grayscale image
  • Trainable segmentation using local features and random forests
  • Watershed segmentation

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• transform
  • interpolation: edge modes
  • fundamental matrix
  • geometric transforms
  • image matching with RANSAC
  • piecewise affine transformations
  • image pyramids
  • radon transforms - sinograms, FBP, SART
  • line model estimation using RANSAC
  • rescale, resize, and downscale
  • structural similarity index
  • swirl effect
  • homographies