Package: bemovi.LEEF 1.1.0

Rainer M Krug

bemovi.LEEF: BEMOVI, software for extracting BEhaviour and MOrphology from VIdeos. This version is adapted for LEEF-UZH

An R and ImageJ based work flow to automatically measure behaviour and morphology from videos. Moving individuals are identified by background subtraction, morphology extracted, and trajectories assembled through time from coordinate data. Abundance, morphology and behaviour can be summarized based on trajectory data.

Authors:Frank Pennekamp <[email protected]>, Owen Petchey <[email protected]>

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bemovi.LEEF/json (API)
NEWS

# Install 'bemovi.LEEF' in R:
install.packages('bemovi.LEEF', repos = c('https://leef-uzh.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/leef-uzh/bemovi/issues

On CRAN:

77 exports 1.38 score 7 dependencies 2 dependents

Last updated 9 months agofrom:a20598c2df (on LEEF). Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 13 2024
R-4.5-winWARNINGSep 13 2024
R-4.5-linuxWARNINGSep 13 2024
R-4.4-winWARNINGSep 13 2024
R-4.4-macWARNINGSep 13 2024
R-4.3-winWARNINGSep 13 2024
R-4.3-macWARNINGSep 13 2024

Exports:anglefuncalculate_mvtcheck_threshold_valuescheck_video_file_namesconvert_cxd_to_aviCreate_folder_structurecreate_overlayscreate_overlays_subtitlecreate_overlays_subtitle_directorycreate_overlays_subtitle_newcreate_overlays_subtitle_singlefilter_datafix_crop_pixelsget_delays_cxdget_duration_aviget_fps_aviget_fps_cxdget_height_aviget_width_aviij.binlink_particlesload_parameterlocate_and_measure_particlesmerge_dataorganise_link_dataorganise_particle_datapar_bfconvertpar_classifier_constantpar_classifier_increasingpar_classifierspar_crop_pixelspar_detect_filterpar_difference.lagpar_disppar_duration_filterpar_extrapolation.factorpar_ffmpegpar_fpspar_heightpar_IJ.pathpar_ijmacs.folderpar_java.pathpar_linkrangepar_masterpar_max_areapar_max_sizepar_mc.corespar_mean_densitypar_median_step_filterpar_memorypar_merged.data.folderpar_merged.data.unfiltered.folderpar_min_areapar_min_sizepar_morph_mvtpar_net_filterpar_overlay.folderpar_particlepar_particle.data.folderpar_pixel_to_scalepar_raw.video.folderpar_showinfpar_species_trackedpar_temp.overlay.folderpar_templatepar_thresholdspar_timeoutpar_to.datapar_to.particlelinkerpar_trajectorypar_trajectory.data.folderpar_video.description.filepar_video.description.folderpar_widthprint_parametersave_parametersummarize_trajectories

Dependencies:bootcirculardata.tableloggitmvtnormsettingsyaml

Readme and manuals

Help Manual

Help pageTopics
Titleanglefun
Bemovi, software for extracting BEhaviour and MOrphology from VIdeos.bemovi
A function to calculate movement metrics for each trajectorycalculate_mvt
Function to assist finding good thresholds used for the segmentation of the difference video. If you run bemovi for the first time, verify with this function that all target objects are properly identified This function creates an ImageJ macro that can be helpful for checking the thresholds specified in the user section; the macro will be saved in the ImageJ macro directory in the working directory and then automatically opened in ImageJ. Depending on the video size, it might take some time to open the video and the thresholding menu. The default thresholds values should be adjusted in the ImageJ macro, until appropriate values are found. These values should then be used in the R functions / script, e.g., when calling the Locate_and_measure_particles function.check_threshold_values
Function to check that video files have extension cxd or avi, and that they are otherwise compatible.check_video_file_names
Function to convert the video files to .avi format using lossless conversionconvert_cxd_to_avi
Create folder structure based on parameterCreate_folder_structure
Function to create a new video with the extracted trajectories overlayed onto the original videocreate_overlays
Function to make overlays using the subtitle files,create_overlays_subtitle
Function to create overlays for all aci files in a directory by using ffmpeg and subtitlescreate_overlays_subtitle_directory
Function to make overlays using the subtitle files,create_overlays_subtitle_new
Function to create a single overlay by using ffmpeg and subtitlescreate_overlays_subtitle_single
Function to filter trajectories based on movement and detection rate characteristicsfilter_data
Fix croppimg parameterfix_crop_pixels
Extract delays from the '.cxd' fileget_delays_cxd
Extract duration in seconds using ffmpegget_duration_avi
Extract fps (frames per second) using ffmpegget_fps_avi
Extract fps (frames per second) from the '.cxd' fileget_fps_cxd
Extract height in pixels using ffmpegget_height_avi
Extract width in pixels using ffmpegget_width_avi
Return ImegeJ executable based on platform. Darwin, Windows and Linux are supportedij.bin
Function to link the particle coordinates through timelink_particles
Load parameter from 'file'load_parameter
Function to extract morphological measurements and X- and Y-coordinates for moving particleslocate_and_measure_particles
Function to create global database containg morphology, trajectory, and video (e.g., experimental) informationmerge_data
Function to merge the output of the ParticleLinker into one large databaseorganise_link_data
Function to merge the morphology and data on X- and Y-coordinates into one file for further processingorganise_particle_data
parameter executable bfconvert of the bftools commandline toolspar_bfconvert
Name of classifier file for constant temperature treatmentpar_classifier_constant
Name of classifier file for increasing temperature treatmentpar_classifiers par_classifier_increasing
Cropping of identified and measured particles.par_crop_pixels
parameter detect_filterpar_detect_filter
parameter difference.lagpar_difference.lag
parameter disppar_disp par_extrapolation.factor
parameter duration_filterpar_duration_filter
parameter executable ffmpegpar_ffmpeg
parameter fpspar_fps
parameter heightpar_height
parameter IJ.pathpar_IJ.path
parameter ijmacs.folderpar_ijmacs.folder
parameter java.pathpar_java.path
parameter linkrangepar_linkrange
Name of Master filepar_master
parameter max_areapar_max_area
parameter max_sizepar_max_size
Number of cores to be used for parallel processing. Defaults to 1, i.e. no parallel processingpar_mc.cores
Name of Mean density per ml filepar_mean_density
parameter median_step_filterpar_median_step_filter
parameter memorypar_memory
parameter merged.data.unfiltered.folderpar_merged.data. unfiltered.folder par_merged.data.unfiltered.folder
parameter merged.data.folderpar_merged.data.folder
parameter min_areapar_min_area
parameter min_sizepar_min_size
Name of Morph_mvt filepar_morph_mvt
parameter net_filterpar_net_filter
parameter overlay.folderpar_overlay.folder
Name of organised particles filepar_particle
parameter particle.data.folderpar_particle.data.folder
parameter pixel_to_scalepar_pixel_to_scale
parameter raw.video.folderpar_raw.video.folder
parameter executable showinf of the bftools commandline toolspar_showinf
Species trackedpar_species_tracked
parameter temp.overlay.folderpar_temp.overlay.folder
Template function to assign value to parameter in the package wide cachepar_template
parameter thresholdspar_thresholds
parameter timeout. If 0, no timeoutpar_timeout
parameter to.data / the base folderpar_to.data
parameter to.particlelinkerpar_to.particlelinker
Name of organised trajectory filepar_trajectory
parameter trajectory.data.folderpar_trajectory.data.folder
parameter video.description.filepar_video.description.file
parameter video.description.folderpar_video.description.folder
parameter widthpar_width
Print the bemovi parameterprint_parameter
Save parameter into '.yaml' filesave_parameter
Function to summarize the morphology, movement and their variability on the trajectory levelsummarize_trajectories