Number and Brightness Image Analysis

ApplyOnPillars | Apply a function to each pillar of a 3-dimensional array. |

ArrArrHexPlot | Plot the values in two arrays against each other. |

BestTau | Find the best tau for exponential filtering detrend. |

Bin2Tiff | Convert a binary image to tiff. |

Brightness | Calculate brightness from image series. |

BrightnessPlotFolder | Make brightness plots (images) for an entire folder. |

BrightnessTimeSeries | Create a Brightness time-series. |

Closest | What's the closest value in a vector? |

CollapseRanges | Collapse a big set of ranges into a smaller set. |

CorrectForBleaching | Detrend an image series |

ExpSmooth | Exponentially smooth a series of observations. |

ExpSmoothPillars | Exponentially smooth pillars of a 3-dimensional array |

FixLUTError | Fix lookup table error when reading images. |

ForceChannels | Fix an image that didn't recognise channels while reading |

GroupClose | Group together close adjacent elements of a vector. |

KmerArray | Get an image where each pixel represents a kmer. |

KmerPlot | A brightness image with a different colour for each kmer. |

KmersFromBrightnesses | Calculate numbers of kmers based on brightnesses |

KmersFromImage | Calculate numbers of kmers based on an image time-series |

KmerTIFFsFromBrightnessCSVs | Create kmer tiff files from brightness csvs |

ListPillars | Turn a 3d array into a list of pillars |

MatrixRasterPlot | Make a raster plot of a matrix. |

MeanIntensity | Calculate mean intensity from image series. |

MeanPillars | Get the means/medians/variances of pillars of a 3d array |

MedianFilterB | Smooth and median filters with options for handling NAs. |

nandb | nandb: Number and brightness in R. |

Number | Calculate number from image series. |

NumberTimeSeries | Create a number time-series. |

PillarsDF | Make each pillar of a 3D array into a column of a tibble |

PillarsListToArr | Make a list of pillars back into a 3D array. |

ReadImageData | Read image as array object. |

SpreadSpecific | Get the best _spread_ of numbers in an interval. |

Stack2DTifs | Put individual tif files into one tif stack. |

WriteImageTxt | Read/write an image array to/from disk as text file(s). |

WriteIntImage | Write an integer array to disk as a tiff image. |

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