Visualize contiguous spixels, color-coded by cellularity.

Visualize individual spixels, color-coded by cellularity.

Visualize results in DSA.

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Yield callback output for one annotation at a time.

Init. This is for PEP compliance.

Init base HTK class.

Init Polygon_merger object. Arguments: --------- maskpaths : list list of strings representing pathos to masks

Init Polygon_merger object. Arguments: --------- contours_df : pandas DataFrame The following columns are needed.

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Init Workflow_runner object. Arguments: --------- slide_iterator : object Slide_iterator object workflow

Init Annotation_iterator object. Arguments: --------- gc : object girder client object slide_id : str

Init Cellularity_Detector_Superpixels object. Arguments: --------- gc : object girder client object slid

Init Cellularity_Detector_Superpixels object. Arguments: --------- gc : object girder client object slide

Recursively add hierarchy levels.

Plot a visualization for rapid review of ROI. This is a callback to be called inside get_all_rois_from_slide_v2(). Parameters ----------

Recursively traverse tree till you get to leafs.

Removes small objects from label image. Parameters ---------- im_label : array_like A uint32 type label image generated by segmen

Run cellularity detection for single slide. The cellularity detection algorithm can either be Cellularity_detector_superpixels or Cellularity

Region-based level sets. Region-based level set implementation based on the Chan-Vese method. Provides cost terms for boundary length, the va

Performs a thinning operation on a label image to remove thin protrusions from objects that are in contact with the background. Applies a dist

Calculates `Fourier shape descriptors` for each objects. Parameters ---------- im_label : array_like A labeled mask image wh

r"""Compute global (i.e., not per-nucleus) features of the nuclei with the given centroids based on the partitioning of the space into Voronoi

Calculates gradient features from an intensity image. Parameters ---------- im_label : array_like A labeled mask image wherein in

Calculate morphometry features for each object Parameters ---------- im_label : array_like A labeled mask image wherein inte

Calculates features for nuclei classification Parameters ---------- im_label : array_like A labeled mask image wherein inten

Computes the fraction of foreground of a single tile or all tiles in a whole slide image given the binary foreground mask computed from a

Connect to a specific girder API. Parameters ---------- apiurl : str URL to the AP to connect to. apikey : str API au

Compute a count of positive pixels in the slide at slide_path. This routine can also create a label image. Parameters ---------- slid

Create and install a Dask distributed client using args from a Namespace, supporting the following attributes: - .scheduler: Address of the d

Discrete Laplacian with edge-value extrapolation. Calculates the discrete Laplacian of an input image. Edge values are calculated by using li

Deletes overlapping regions from an image label based on overlap information and tile size. Args: ---- im_label (ndarray): Image

Performs a nuclear segmentation using kofahi's method. This method uses scale-adaptive multi-scale Laplacian-of-Gaussian filtering for blob e

Detect nuclei within a tile image and generate annotations. Args: ---- tile_info (dict): Information about the tile image.

Computes a label mask highlighting a ring-like neighborhood of each object or region in a given label mask Parameters ---------- im_l

Converts time from seconds to a string of the form hours:minutes:seconds

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Dump annotations for single slide into the local folder. Parameters ---------- gc : girder_client.GirderClient authenticated gird

Calculates the eigenvectors of the hessian volumes 'H' generated by Hessian.py Parameters ---------- im_hess : array_like

Embeds object boundaries into an RGB color, grayscale or binary image, returning a color rendering of the image and object boundaries. Ta

Exclude columns from m that have infinities or nans. In the context of color deconvolution, these occur in conversion from RGB to SDA when th

Generates a Poisson mixture model to fit pixel intensities for foreground/background masking. Takes as input an array or intensity image 'I'

Performs smoothing with derivative gaussian kernel. Uses separable convolution to simultaneously smooth and calculate the gradient of a grays

Performs nuclear detection using Gaussian kernel voting. Uses a gaussian kernel to localize the centroids of cell nuclei. Takes as input a he

Take a matrix m (probably 3xN) and return the 3x3 matrix of "principal components". (Actually computed with SVD)

Return a dict corresponding to region, checking the region size if maxRegionSize is provided. The intended use is to be passed via **kwargs,

Get the stain matrix corresponding to the args.stain_$index and args.stain_$index_vector arguments for values of index 1 to count. Return a nu

Yield an authenticated girder client that points to the server. If a local girder server docker is running, this will connect to it, oth

Performs generalized Laplacian of Gaussian blob detection. Parameters ---------- im_input : array_like A hematoxylin intensity im

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Performs gradient-field tracking to segment smoothed images of cell nuclei. Takes as input a smoothed intensity or Laplacian-of-Gaussian fil

Calculates hessian of image I convolved with a gaussian kernel with covariance C = [Sigma^2 0; 0 Sigma^2]. Parameters ----------

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Local max clustering pixel aggregation for nuclear segmentation. Takes as input a constrained log or other filtered nuclear image, a binary nu

Processes boundary coordinates in polyline with vertices X, Y to remove redundant colinear points. Polyline is not assumed to be open or closed.

Merges attraction basins obtained from gradient flow tracking using sink locations. Parameters ---------- Segmentation : array_l

Performs a nuclear segmentation using a gradient contour tracing and geometry splitting algorithm. Implemented from the reference below. Para

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Parse loaded annotations for slide into tables. Parameters ---------- item : dict girder response with item information anno

Converts a label or binary mask image to a binary perimeter image. Uses 4-neighbor or 8-neighbor shifts to detect pixels whose values do not

Convert a set of region polygons to a numpy binary mask. Params ------ polygons: list A list of lists of x, y tuples. If None, r

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Query by a point.

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Return things that intersect with 'r'.

Constructs a region adjacency graph for a label image using either 4-neighbor or 8-neighbor connectivity. Background pixels are not included (

Adds an additional layer of dependence to a region adjacency graph, connecting each node to the neighbors of its immediate neighbors. Paramet