Changes in version 1.15.4 (2024-03-21) o measureObject fix reversion and test - Bioc 3.19 Changes in version 1.15.3 (2024-03-13) o measureObject fixes for Bioc 3.19 release Changes in version 1.15.2 (2023-12-13) o change of package maintenance to Lasse Meyer Changes in version 1.15.1 (2023-12-10) o the unit tests for compImage have now been adjusted to account for correct spillover induction Changes in version 1.13.1 (2023-09-26) o loadImages: fixed pattern argument to only test on the actual files and not the path. Changes in version 1.11.3 (2023-01-23) o loadImages: added option to read in single-channel images to multi-channel Changes in version 1.11.2 (2023-02-02) o Bug fix: measureObjects internally sets the correct channel names Changes in version 1.11.1 (2023-01-18) o Bug fix: set default dodge.width = NULL for geom_quasirandom Changes in version 1.9.2 (2022-10-24) o measureObjects accounts for single objects in images Changes in version 1.9.1 (2022-07-24) o measureObjects function transfers mcols of images and masks to colData(sce) o allow returned object to be of SpatialExperiment Changes in version 1.7.2 (2022-04-20) o Fixes for next release Changes in version 1.7.1 (2021-12-28) o Added compImage function for channel spillover compensation Changes in version 1.5.4 (2021-09-17) o It is not required anymore to specify exactly the right colours Changes in version 1.5.3 (2021-09-16) o Added option to read in .h5 files Changes in version 1.5.2 (2021-09-15) o Added description on how to handle images with couplet/patchwork Changes in version 1.5.1 (2021-05-19) o Bugfix: erroneous dimension setting when legend=NULL Changes in version 1.3.6 (2021-04-23) o scaleImages accepts numeric vector value Changes in version 1.3.5 (2021-04-07) o Added measureObjects function Changes in version 1.3.4 (2021-03-20) o Support on disk representation of images Changes in version 1.3.3 (2021-01-24) o Added snapshot tests for shiny o Support win32 again Changes in version 1.3.2 (2021-01-12) o Updated citation Changes in version 1.3.1 (2020-12-01) o Allow thick border contours Changes in version 1.1.6 (2020-10-23) o Dropped 32-bit Windows support Changes in version 1.1.5 (2020-10-11) o Prepared for Bioc 3.12 release o Started unit testing the shiny app Changes in version 1.1.4 (2020-09-13) o Allow channel-specific inputRange inputs for normalisation Changes in version 1.1.3 (2020-09-12) o Extended vignette o Changed package title Changes in version 1.1.2 (2020-07-17) o Added shiny app to package Changes in version 1.1.1 o Images are no longer re-normalized after channel merging (> 3 channels) o Instead images are clipped at 1 leading to brighter colours o The same happens for colour merging when colouring masks by feature expression Changes in version 0.99.5 (2020-04-10) o Added script to generate the toy dataset o Modified the toy dataset o Added more explanation on datasets to vignette o Bug fixes when colouring cells o Unit tests on all hidden functions o Account for over-saturation when merging colours o Fixed labelling of colour legends o Corrected typos in docs and vignette o Avoid recalculation of min/max values in legend function Changes in version 0.99.4 (2020-04-01) o Fixed docs to pass checks on Windows o Aesthetic changes to scale bar, image title and legend title o Removed channelNames as Image generic o removed exported plot method Changes in version 0.99.0 (2020-03-30) o Formatted the package for Bioconductor submission Changes in version 0.1.13 (2020-03-28) o Full vignette and correction to docs Changes in version 0.1.12 (2020-03-25) o Renamed package from SingleCellMapper to cytomapper o Renamed ImageList class to CytoImageList class Changes in version 0.1.11 (2020-03-24) o Complete documentation of all package functions Changes in version 0.1.10 (2020-03-21) o interpolate parameter o Bug fix to achieve correct aspect ratios Changes in version 0.1.9 (2020-03-20) o scale, return_plot, return_images, legend, margin, display parameters o Finalised unit tests Changes in version 0.1.8 (2020-03-18) o Option to remove legend o Cleaned up representation of legend on plot Changes in version 0.1.7 (2020-03-17) o Added scaleImages and normalize functions o Expanded shared parameters for plotPixels and plotCells Changes in version 0.1.6 (2020-03-10) o Unit tests on plotCells and plotPixels o Improved setting colours o Rewrite to reduce validity checks Changes in version 0.1.5 (2020-03-03) o plotCells function o plotPixels function o Options for further customization of scale_bar o Options for image_title customization o Started vignette draft Changes in version 0.1.4 (2020-02-16) o Full docs and test on: - loadImages - ImageList-class Changes in version 0.1.3 (2020-02-16) o Full docs and tests on: - ImageList-naming - ImageList-subsetting Changes in version 0.1.2 (2020-02-03) o channelNames generic function for Image and ImageList object o Reduced the size of example data o Wrote docs on data Changes in version 0.1.1 (2020-02-02) o Simplified structure of loadImages function o Created validity checks for path and file inputs o Fixed bugs to pass R CMD check o test Changes in version 0.1.0 (2020-01-16) o Initial commit o Creation of the SingleCellMapper package o Created inst/extdata folder with example images and data o Build the ImageList class o Created first unit tests for ImageList constructor o test