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Find regions that are potentially cellular.

Identify the stain vector in w that best aligns with the reference vector. This is used with adaptive deconvolution routines where the order of r

Keep largest and most cellular regions.

Fix self.GTcodes (important!).

Generates N visually distinct RGB colors Parameters ---------- n : int Number of distinct RGB colors to output seed: in

Get all rois in a girder folder using get_all_rois_from_slide_v2(). Parameters ---------- gc : girder_client.Girder_Client authen

Get concatenated contours and overall bounding box. Returns ------- - pandas DataFrame: has the same structure as output from

Given a binary mask, get opencv contours. Parameters ---------- bin_mask : nd array ground truth mask (m,n) - int32 with [0, 1] v

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Parse region from the slide and get its corresponding labeled mask. This is a wrapper around get_roi_mask() which should be referred to for i

Get final merged shapely multipolygon by hierarchical merger.

Convert the region into a list of polygons. Params ------ region: list 4 elements -- left, top, width, height -- or all -1,

Given dataframe of contours, get annotation document. This uses the large_image annotation schema to create an annotation document that maybe

Get the stain corresponding to args.stain_$index and args.stain_$index_vector. If the former is not "custom", all the latter's elements must

Diffusion of gradient field using Navier-Stokes equation. Used for smoothing/denoising a gradient field. Takes as input a gradient field

Computes gray-level co-occurence matrix (GLCM) within a region of interest (ROI) of an image. GLCM is a 2D histogram/matrix containing the cou

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Initialize labeled components mask.

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Transforms an image from LAB to RGB color space Parameters ---------- im_lab : array_like An image in LAB color space Return

Constructs a label image from scored contours. Masks for contours with low priority/score are placed first into the label image and then are o

Scores the length of the cutting line (x1, y1)->(x2, y2) made at a concavity depth of d1 and d2. Returns ------- Score : float

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Get the magnitude of each column vector in a matrix

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Normalize each column vector in a matrix

Fast, vectorized IoU. Source: https://medium.com/@venuktan/vectorized-intersection-over-union ... -iou-in-numpy-and-tensor-flow-4fa16

Perturb stain concentrations in SDA space and return augmented image. This is an implementation of the method described in Tellez et al, 2018

Process nuclei feature extraction and annotation from an input image. Args: ---- args (dict): Configuration parameters for featu

Read nuclei feature data from a specified file. Args: ---- args (dict): Configuration parameters including the input feature fil

Dump annotations into single slide from local folder (Internal function). Parameters ---------- gc : girder_client.GirderClient a

Only keep relevant part of slide mask.

Only keep relevant part of slide mask.

Revert all annotations in a slide to a previous version. Parameters ---------- gc : girder_client.GirderClient authenticated gird

Rotate a certain point list around a central point. Modified from. javascript version at: https://github.com/girder/large_image/blob/master/

Run full pipeline to get merged contours. Returns ------- - pandas DataFrame: has the same structure as output from g

Run sequence for merging polygons & adding contours.

Get cellularity and optionally visualize on DSA.

Run full pipeline to detect cellular regions.

Get cellularity and optionally visualize on DSA.

Run cellularity detection and optionally visualize result. This runs the cellularity detection +/- visualization pipeline and returns

Run sequence for merging polygons & adding contours (one group).

Scores boundary contours using gradient information. Implemented from the reference below. Each contour is weighted by the average gradient and

Detects seed pixels for contour tracing by finding max-gradient points between local minima and maxima in an intensity image. Parameters

Compute the stain matrix for color deconvolution with the Macenko method. For a two-stain image or matrix in SDA space, this method works by

Compute the stain matrix for color deconvolution with SNMF. ... (sparse non-negative matrix factorization). Parameters ---------- im

Set color normalization values for thumbnail or main image.

Get contours_df from all masks. This is a wrapper around get_contours_from_mask(), with the added functionality of separating out con

Slice a single group from self.contours_df.

Get hierarchy of node indices.

Go through each group and merge contours. Sets: - self.merged_contours: pandas DataFrame: has the same structure as output fr

Set reference values and configuration parameters for feature extraction. Args: ---- args (dict): Configuration parameters for f

Get dictionary of roi bounding boxes. Arguments: --------- - roi_offsets: dict (default, None): dict indexed by maskname,

Get shared edges between rois in same slide (Internal).

Set self.slide_info dict and self.labeled tissue mask.

Set self.slide_info dict and self.labeled tissue mask.

Fit gaussian mixture model to features and get assignment.

Get superpixel features.

Use Simple Linear Iterative Clustering (SLIC) to get superpixels.

Load RGB from server for single tissue piece.

Load RGB from server for single tissue piece.

Get tree in convenience dict format (dicts inside dicts).

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Performs segmentation of the foreground (tissue) Uses a simple two-component Gaussian mixture model to mask tissue areas from background in br

Performs splitting of objects in a label image using geometric scoring of concavities. Attempts to perform splits at narrow regions that are p

Performs contour tracing of seed pixels in an intensity image using gradient information. Parameters ---------- I : array_like

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Update permissions for all annotations in a slide. Parameters ---------- gc : girder_client.GirderClient authenticated girder cli

Update styles for all annotations in a folder recursively. Parameters ---------- gc : girder_client.GirderClient authenticated gi

Update styles for all annotations in a slide. Parameters ---------- gc : girder_client.GirderClient authenticated girder client