Up: Components summary Author

Ville Rantanen

Component Version Inputs Outputs Description
AlphaShape 1.1 in out Takes a list of points and returns the alpha shape.
Array2CSV 1.1 in, relative out Reads an array, and returns a CSV with Key and File columns.
Array2Folder 1.2 in, template out Transforms an array into a physical folder.
ArraySplit 1.1 in out1, out2, out3, out4, out5, out6, out7, out8, out9 Divides array keys evenly in to N arrays.
BackgroundSubtract 1.1 in, opt out Performs background subtraction for a directory of images with various methods.
BashEvaluate 1.4.2 array1, array2, array3, command, var1, var2, var3, var4, var5, var6, vararray scriptOut, stdOut, stdErr, out1, out2, out3, folder1, folder2, folder3, arrayOut1, arrayOut2, arrayOut3 Executes a Bash script that generates any output from the given data or other inputs.
BFConvert 1.0 in out Wrapper for the Bioformats command line tool for converting exotic image formats.
BFMetadata 1.0 in raw, ome Wrapper for the Bioformats command line tool for extracting metadata from exotic image formats.
BlobDraw 0.1 images, objects, names out Visualizes the blobs found in a directory of images.
BlobFeatures 0.1 images, objects, names out reads the blobs found in a directory of images and produces intensity features The component requires that all the columns from ImageBlobDetect are still found in the data file.
CellProfiler 1.0 pipeline, in1, in2, in3, in4, in5, in6, in7, in8, in9 out1, out2, out3, out4, out5, out6, out7, out8, out9, pipelineDebug Runs a pipeline in CellProfiler, for a folder or several folders of images.
ClassifierPerformance 1.0 in out Calculates popular classifier performance values based on actual classes, and predicted values.
ClickImage 1.2 in out Get user to click points on a folder of images, and write a CSV table of the coordinates.
ClusterPlot 1.0 in, plotSpec out Generates 2D plots for clusters where the dimensions are specified, hence specializing the pairwise plotting of all possible pairs of clusters dimensions.
ClusterReorder 1.0 in out Re-orders cluster ID numbers based on a given data vector.
CombinationCounter 1.1 in out, ratios Count the occurrencies of combinations of two labels.
CompareImage 0.3 expected, image Compare images.
ConvertImage 1.2 in, inArray outArray, out, list Reads various image formats with LOCI Bioformats library (http://www.loci.wisc.edu/software/bio-formats).
CopyOutput 1.1 in Copies any input to a user selected path.
CSV2Array 1.1 in out Reads a CSV, and returns an array based on selected columns.
CSV2Image 1.2 in, reference out, frequency Create an image visualization from CSV file.
CSVSplit 1.0 in out Divides the content of the given CSV to an array of multiple CSV files.
CSVSummary 1.1 in out Summarises values for rows of a file according to a column label or the whole file to single row.
Ellipse2Mask 1.0 images, objects, names mask, perimeter, masklist Converts a CSV expression of ellipses in to masklist (and mask) image format.
EnsembleAttributeSelection 1.0 in out Feature selection with multiple algorithms.
FCSReader 1.0 in, annotations out, metadata FCSReader imports a FCS file (standards 2.0 and 3.0 supported) and converts it into a tab-delimitted CSV file.
FolderCleaner 1.2 in, inArray out, outArray Renames a folder of files, by leaving only the last extension.
FolderSplit 1.1 in out Divides files evenly from a folder in to N folders in an array.
GMLVQClassifier 1.1 data, testData, classifyData, inClassifier outClassifier, confusion, importances, evaluation, predictedClasses Trains a classifier based on the given sample data, or predicts with a classifier trained earlier.
GNUPlot 0.5 in, script, optScript scriptOut, out Executes a GNUPlot script that generates any output from the given data or other inputs.
GUIInput 1.0 template, defaultValues out, saved Asks user for inputs.
HistogramPlot 1.1 in, plotAnnotator frequencies, midpoints, out Counts the frequencies and makes a line plot of histogram values.
HistogramPlot_FrequencyCalculator 1.0 in out, midPoints, breakPoints, midPointsFormatted Calculates frequencies from data to be used in a HistogramPlot.
HTMLImages 1.0 in, menuChoices, css out Creates a static list of images to a web page.
Image2CSV 1.1 in, mask out Create a CSV file from image file.
ImageGallery 2.0 inArray, inRoot, csvRoot, csvArray, infoRoot, style out Creates a web gallery from given folders of images and optional annotation CSV files.
ImageList2MaskList 1.0 in out, mask, perimeter Convert from ImageList type to MaskList data type.
ImageList2Video 1.1 in out Uses either ImageMagick or avconv to convert a list of images in to a video file.
ImageLocalMaxima 1.2 in, names mask, centers Finds local maxima centers in a grayscale intensity image.
ImageMagick 1.2 ina1, ina2, in1, in2, in, commandFile, f1, f2 out A versatile wrapper for using ImageMagick convert, for folder(s) of images.
ImageSummary 1.0 gray, mask, names out Summarises a directory of images, with one line for each image.
IntensityCorrelation 1.0 image1, image2, mask, names out, plot Extracts the intensity correlation features (Co-Localization) from two image channels.
IntensityFeatures 2.3 images, mask, names, masklist edges, out Extracts the intensity features from segmented image mask and gray scale image.
Labels2Columns 1.1 in out Reads columns of data, the unique entries of the label column are transposed as column names.
LinearBinner 1.0 in binned, cluster A very basic clustering-like method.
LinearNormalizer 1.0 in out Normalizes the input matrix column-wise.
LineFeatures 1.0 lines, images, names out Measure LinkedList segments as objects.
MaskClusterDraw 1.0 mask, clusters, images, names out Reads cluster id:s, images and masks to create a colored visualization of object clustering.
MaskFilter 1.1 inMask, objects, names mask, perimeter Filters mask objects based on the object numbers present in a table.
MaskList2ImageList 1.0 in out Copy files from MaskList image structure to conventional ImageList data type.
MaskRelate 1.2 parent, child, names out, overlap Relates objects from two masks defining parents and their children objects.
MatlabEvaluate 1.0 script, table1, table2, table3, table4, table5, var1, var2, var3, var4, var5, var6, var7, var8, var9 table, optOut1, optOut2, optOut3, document Executes a Matlab script that generates a matrix from the given data.
MatlabOp 1.2 command, table, in1, in2, in3, in4, in5, inArray, file1, file2 out, out2, tableOut Executes a Matlab script that generates an image directory from given image directories.
MergeImage 1.2 in out Joins grayscale images together with colors of choice.
MorphologyFeatures 2.2 mask, names, masklist out, skeleton Extracts the morphology features from segmented image mask.
MRXSConvert 1.1 in out, label Exports MRXS images in to PNGs, cropping them to small images.
NucleusGenerator 1.0 out, centers Generates DAPI-like grayscale images with random cell nuclei.
ObjectFilter 1.0 mask, objects, names out Filters objects based on the object X,Y coordinates and an overlap with a mask image.
Pandoc 1.0 in, header, before, after, attachment out Executes Pandoc with user given switches.
PCA 1.1 matrix loadings, scores, variation PCA performs a principal component analysis on a given data matrix based on eigen values.
PhenographClusterer 1.0 in out, graph Clusters data using Phenograph clustering method.
PipelineInput 1.1 name, n Read a previous Anduril pipeline execution folder as an input.
PlotHTML 0.1 data, template plot Creates scatter, line or bar plots where Y and X coordinates come from JSON files.
PointDistance 1.1 in, reference out Measures the nearest reference point (reference) distance for each input point (in).
PointTracker 1.0 in out Tracks point coordinates moving in time giving an ID for each track.
PythonEvaluate 0.5 scriptIn, table1, table2, table3, table4, table5, var1, var2, var3, inArray, folder, vararray table, outArray, out1, out2, out3 Executes an Python script.
QuickBash 1.0 in, command out Executes a Bash script that generates any output from the given data or other inputs.
Rsync 1.0 inFile, inFolder outFile, outFolder Uses rsync to fetch or push files.
SampleBalancer 1.0 in balanced, remainder Divides matrix rows in to two, by balancing the occurrence of unique labels in column.
SegmentBlob 0.1 in, names out Segment a directory of images with Gaussian Blob method.
SegmentCRImage 1.0 in mask, perimeter, features Segments a directory of images with a method tuned for HE images.
SegmentGraphCut 1.1 in mask, perimeter Segmentation based on graph cutting.
SegmentImage 2.3 in, opt, seed mask, perimeter, numbered, masklist Segments a directory of images with various methods.
SegmentSeeded 1.0 in, seed, colors mask, perimeter, numbered Segments a directory of images with various methods, using a seed (a previous mask helping in refining the segmentation).
SequencingRequirements 1.0 This component depends on the requirements required by the functions in this bundle.
ShapeFitting 0.1 images, shape, names limits, location, orientation, scale Fits a user given shape on image data by changing the location, orientation and scale of the shape.
SimpleWebPage 1.3 in, inArray, content, style, annotation, tableArray out Creates a simple web page, for publishing a list of files.
Skeleton2CSV 1.0 in, names out Extracts lines from a skeleton mask.
SkeletonFeatures 1.0 skeleton, images, names out, points Extracts intensity information from a grayscale image, using a skeleton mask.
SpiralJoin 1.0 in out Joins grayscale images together in a montage, or splits a montage in to separate images in a spiral fashion.
StackProjection 1.0 in, toMap out, map, mapped Projects a grayscale z-stack to a 2D image.
SyntaxHighlight 1.1 in HTML, image, latex Reads a program code listing, and creates a syntax highlighted HTML file.
TextDraw 1.1 images, text, names out Write text on a bitmap image with a small font.
TextureFeatures 1.0 in, names images, out The component uses VLFeat library to extract SIFT/MSER keypoints and SIFT descriptors from grayscale images.
Video2ImageList 1.0 in out Uses either ImageMagick or avconv to convert a list of images in to a video file.
Watershed 2.0 images, seed mask, lines, perimeter Methods to divide objects in a mask, or grayscale images.

Generated 2019-01-14 07:42:05 by Anduril 2.0.0