| 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. |
Up: Components summary
Ville Rantanen