NEWS
flowcatchR 1.20.0
Bug fixes
- In the
shinyFlow app, include.area now defaults to FALSE
flowcatchR 1.16.0
Other notes
- The project website based on
pkgdown has been created and published on GitHub
- Added a
NEWS.md file to track changes to the package.
flowcatchR 1.15.2
New features
- Initial submit to Bioconductor.
flowcatchR 1.14.0
New features
- the engine for plotting the trajectories is now based on plotly, abandoning the older rgl-based solution
Other notes
- vignette: now also based on Rmarkdown, leaving the older Rnw-pdf be
- shortened example lines for better documentation
- better definition of import statements for better behaviour with other packages
- updated travis.yml for current setup
flowcatchR 1.4.0
New features
- added details in the vignette on the dockerflow proposal, where flowcatchR is made available in preconfigured Docker containers
Bug fixes
- penaltyFunctionGenerator: simmetric penalty function is now correctly computed
Other notes
- added LazyData: true in the DESCRIPTION
- updated travis.yml to use native R integration
- vignette: improved structure, to enhance readability and usability; removed rgl hook which was not used anyway
- documentation: slight updates and enhancements
flowcatchR 1.2.0
New features
- addTrajectory: changed implementation in the addTrajectory function, notable gain in computing time
- particles: implementation of particles() now used BiocParallel - massive gain in performances!
- snap() function to allow interaction of the user with the image, to display additional information on the trajectories identified on the Frames/ParticleSet
- shinyFlow() released! A Shiny App is delivered along with the package, documentation is available to guide exploration of data and parameters
- Jupyter/IPython notebooks available in the installed folder of the package - provided as template for further analysis
- Vignette: updated to reflect the current implementation and newest features
- preprocess.Frames: extended documentation
- BiocViews: added a couple of terms that fit better with current status of the package
- Added url for development version on github. Active development is performed there, therefore feel free to send pull requests/feature wishes (https://github.com/federicomarini/flowcatchR/issues)!
- Added integration of the repository with Travis-CI
- add.contours: if image is in grayscale, use false colours to enhance detected particles
- plot2d.TrajectorySet is now able to draw a grid and help backtracking points from the trajectories
Bug fixes
- select.Frames: fixed behaviour in select.Frames when selecting a single frame
- add.contours: corrected bug in add.contours for grayscale images, was preventing correct combining of images. now uses correctly false colours and aids identification
- particles: for computing particles,added check whether dimnames is set or not. previously it raised an error, but it was kind of overkilling
- fixed behaviour in export.Frames
- typos fixed
- Vignette: fixed typos, fixed parameter names in the preprocessing steps
- read.Frames: additional check on the existence of all files
- Grayscale images can now be directly preprocessed by selecting channel = "all"
flowcatchR 1.0.3
New features
- addTrajectory: changed implementation in the addTrajectory function, notable gain in computing time
- particles: implementation of particles() now used BiocParallel - massive gain in performances!
- snap() function to allow interaction of the user with the image, to display additional information on the trajectories identified on the Frames/ParticleSet
- shinyFlow() released! A Shiny App is delivered along with the package, documentation is available to guide exploration of data and parameters
- Jupyter/IPython notebooks available in the installed folder of the package - provided as template for further analysis
- Vignette: updated to reflect the current implementation and newest features
- preprocess.Frames: extended documentation
- BiocViews: added a couple of terms that fit better with current status of the package
flowcatchR 1.0.2
Bug fixes
- select.Frames: fixed behaviour in select.Frames when selecting a single frame
- add.contours: corrected bug in add.contours for grayscale images, was preventing correct combining of images. now uses correctly false colours and aids identification
- particles: for computing particles,added check whether dimnames is set or not. previously it raised an error, but it was kind of overkilling
- fixed behaviour in export.Frames
- typos fixed
flowcatchR 1.0.1
New features
- Added url for development version on github. Active development is performed there, therefore feel free to send pull requests/feature wishes (https://github.com/federicomarini/flowcatchR/issues)!
- Added integration of the repository with Travis-CI
- add.contours: if image is in grayscale, use false colours to enhance detected particles
- plot2d.TrajectorySet is now able to draw a grid and help backtracking points from the trajectories
Bug fixes
- Vignette: fixed typos, fixed parameter names in the preprocessing steps
- read.Frames: additional check on the existence of all files
- Grayscale images can now be directly preprocessed by selecting channel = "all"
Other notes
flowcatchR 1.0.0
New features
- Initial release to Bioconductor!
flowcatchR 0.99.4
New features
- Final fixes. Accepted in the current status at Bioconductor.
flowcatchR 0.99.3
New features
- Changes in the code to be adapted to the latest devel version of EBImage (new functions were added for the Frames class).
flowcatchR 0.99.2
New features
- Updated/added documentation.
flowcatchR 0.99.1
New features
- Adapted after first round of review.