NEWS

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cytomapper 1.15.4 (2024-03-21)

• measureObject fix reversion and test - Bioc 3.19

cytomapper 1.15.3 (2024-03-13)

• measureObject fixes for Bioc 3.19 release

cytomapper 1.15.2 (2023-12-13)

• change of package maintenance to Lasse Meyer

cytomapper 1.15.1 (2023-12-10)

• the unit tests for compImage have now been adjusted to account for correct spillover induction

cytomapper 1.13.1 (2023-09-26)

• loadImages: fixed pattern argument to only test on the actual files and not the path.

cytomapper 1.11.3 (2023-01-23)

• loadImages: added option to read in single-channel images to multi-channel

cytomapper 1.11.2 (2023-02-02)

• Bug fix: measureObjects internally sets the correct channel names

cytomapper 1.11.1 (2023-01-18)

• Bug fix: set default dodge.width = NULL for geom_quasirandom

cytomapper 1.9.2 (2022-10-24)

• measureObjects accounts for single objects in images

cytomapper 1.9.1 (2022-07-24)

• measureObjects function transfers mcols of images and masks to colData(sce)
• allow returned object to be of SpatialExperiment

cytomapper 1.7.2 (2022-04-20)

• Fixes for next release

cytomapper 1.7.1 (2021-12-28)

• Added compImage function for channel spillover compensation

cytomapper 1.5.4 (2021-09-17)

• It is not required anymore to specify exactly the right colours

cytomapper 1.5.3 (2021-09-16)

• Added option to read in .h5 files

cytomapper 1.5.2 (2021-09-15)

• Added description on how to handle images with couplet/patchwork

cytomapper 1.5.1 (2021-05-19)

• Bugfix: erroneous dimension setting when legend=NULL

cytomapper 1.3.6 (2021-04-23)

• scaleImages accepts numeric vector value

cytomapper 1.3.5 (2021-04-07)

• Added measureObjects function

cytomapper 1.3.4 (2021-03-20)

• Support on disk representation of images

cytomapper 1.3.3 (2021-01-24)

• Added snapshot tests for shiny
• Support win32 again

cytomapper 1.3.2 (2021-01-12)

• Updated citation

cytomapper 1.3.1 (2020-12-01)

• Allow thick border contours

cytomapper 1.1.6 (2020-10-23)

• Dropped 32-bit Windows support

cytomapper 1.1.5 (2020-10-11)

• Prepared for Bioc 3.12 release
• Started unit testing the shiny app

cytomapper 1.1.4 (2020-09-13)

• Allow channel-specific inputRange inputs for normalisation

cytomapper 1.1.3 (2020-09-12)

• Extended vignette
• Changed package title

cytomapper 1.1.2 (2020-07-17)

• Added shiny app to package

cytomapper 1.1.1

• 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

cytomapper 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
• Fixed labelling of colour legends
• Corrected typos in docs and vignette
• Avoid recalculation of min/max values in legend function

cytomapper 0.99.4 (2020-04-01)

• Fixed docs to pass checks on Windows
• Aesthetic changes to scale bar, image title and legend title
• Removed channelNames as Image generic
• removed exported plot method

cytomapper 0.99.0 (2020-03-30)

• Formatted the package for Bioconductor submission

cytomapper 0.1.13 (2020-03-28)

• Full vignette and correction to docs

cytomapper 0.1.12 (2020-03-25)

• Renamed package from SingleCellMapper to cytomapper
• Renamed ImageList class to CytoImageList class

cytomapper 0.1.11 (2020-03-24)

• Complete documentation of all package functions

cytomapper 0.1.10 (2020-03-21)

• interpolate parameter
• Bug fix to achieve correct aspect ratios

cytomapper 0.1.9 (2020-03-20)

• scale, return_plot, return_images, legend, margin, display parameters
• Finalised unit tests

cytomapper 0.1.8 (2020-03-18)

• Option to remove legend
• Cleaned up representation of legend on plot

cytomapper 0.1.7 (2020-03-17)

• Added scaleImages and normalize functions
• Expanded shared parameters for plotPixels and plotCells

cytomapper 0.1.6 (2020-03-10)

• Unit tests on plotCells and plotPixels
• Improved setting colours
• Rewrite to reduce validity checks

cytomapper 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

cytomapper 0.1.4 (2020-02-16)

• Full docs and test on: - loadImages - ImageList-class

cytomapper 0.1.3 (2020-02-16)

• Full docs and tests on: - ImageList-naming - ImageList-subsetting

cytomapper 0.1.2 (2020-02-03)

• channelNames generic function for Image and ImageList object
• Reduced the size of example data
• Wrote docs on data

cytomapper 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

cytomapper 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