NEWS.md

In flowcatchR: Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells

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 1.14.0

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.

flowcatchR 1.15.2

New features

• Initial submit to Bioconductor.

flowcatchR documentation built on Nov. 8, 2020, 5:04 p.m.