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