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.

Changes in version 1.15.1 (2023-12-10):
+ the unit tests for compImage have now been adjusted to account for correct spillover induction

Changes in version 1.15.2 (2023-12-13):
+ change of package maintenance to Lasse Meyer

Changes in version 1.15.3 (2024-03-13):
+ measureObject fixes for Bioc 3.19 release

Changes in version 1.15.4 (2024-03-21):
+ measureObject fix reversion and test - Bioc 3.19
