Tracking Algorithms for Phagocytes
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figures Add files via upload Apr 19, 2018
.gitignore Upgrade for neutrophil movie generation + minor changes Mar 23, 2017
COPYING plotTrackStats and plotNeutrophilMovie Jul 14, 2015
LICENSE plotTrackStats and plotNeutrophilMovie Jul 14, 2015
README.md Added reference to Wiki for User Manual Jun 4, 2018
RedGreenChannels.png Add files via upload Apr 19, 2018
assignParentLoop.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
assignParentOverlap.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
branchPoints.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
breakOneTrack.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
cleanNetwork.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
concatenateNodes.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
createString.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
deleteMultipleTracks.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
detectNeutrophilCollision.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
determineDataStructure.m Dev (#6) May 4, 2017
displayActivationPoint.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
displayMaps.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
distanceElements.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
drawsquare_r.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
effectiveDistance.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
effectiveTracks.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
endPoints.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
expandu.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
exportTracksToICYxml.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
findTailBoundary.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
fixhandlesdir.m Merge branch 'master' into dev Jul 3, 2017
gaussF.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
getDistanceNet.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
getDistanceNetForTracks.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
getMatFolders.m Dev (#6) May 4, 2017
importTracksFromICYxml.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
joinMultipleTracks.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
joinTwoTracks.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
linkEndStartTracks.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
linkLostNeutrophil.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
linkTracks.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
metricPositionMap.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
microChipAnalysis.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
neutrophilAnalysis.m Dev (#6) May 4, 2017
neutrophilOverlap.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
padData.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
plotNeutrophilMovie.m support for movie creation Mar 31, 2017
plotTrackStats.m Select3D and new track displays Sep 15, 2015
plotTracks.m FIXED: colorbar's colourmap in option typeOfPlot=2 of plotTracks (#3) Mar 30, 2017
plotTracksAndFrame.m Merge branch 'master' into dev Jul 3, 2017
positionNeutrophil.m Minor changes. Jul 3, 2017
readNeutrophils.m fix error in reading Jul 26, 2018
reduceNeutrophil.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
reduceu.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
removeHandlesFields.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
removeMultipleTracks.m from dev (#5) Apr 24, 2017
removeOneTrack.m from dev (#5) Apr 24, 2017
select3d.m Select3D and new track displays Sep 15, 2015
selectNeutrophilsM.m [selectNeutrophilsM] WARNING of EraseMode Mar 31, 2017
setNeutrophilHandles.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
shadingCorrection.m StopCriterion shadingCorrection Jul 24, 2015
shapeNeutrophil.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
splitLargeNeutrophil.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
splitNeutrophilCollision.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
testKeyHole.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
thresNeutrophil.m Select3D and new track displays Sep 15, 2015
trackNeutrophil.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
trackOrientation.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
verifyThresholdNeutrophils.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015
visualiseTracksAndFrames.m from dev (#5) Apr 24, 2017
zerocross.m plotTrackStats and plotNeutrophilMovie Jul 14, 2015

README.md

Phagosight

Tracking Algorithms for Phagocytes and other moving objects.

Installation

After cloning the repository, it is important to add it (with subfolders) to the Matlab path. Full manual and instructions can be found here.

Usage and Quick Start

Phagosight can be used with the help of a GUI that allows the user to select manually the folder where the data is in. This is done by the command

[handles] = neutrophilAnalysis();

The program can be fully automatic, the user knows some or all the parameters. An example of this:

[handles] = neutrophilAnalysis('/path/to/data/', 0, [], [0.2 0.4]);

where parameters not known, or that want to be taken by default, are simply set to empty arrays []. For a detailed review of the input parameters, the help command outputs all the information the user might need.

help neutrophilAnalysis

User Manual

For a detailed and comprehensive user manual, check the Wiki section.

Output and results

Phagosight returns variable handles, which contains information about the tracks and locations where results from intermediate steps are stored. For example, if the path to data is a folder with name Data/, then the new folders created:

  • Data_mat_Or Stores the original data in Matlab's own .mat format.
  • Data_mat_Re Stores the data after preprocessing, whether it is reduction by subsampling or filtering (if size is not reduced)
  • Data_mat_La Stores the labelled data after segmentation.

Citation

Phagosight is released under the GNU General Public License v3. Please cite Phagosight in your publications if it helps your research:

@article{Henry2013,
 author = {Henry, Katherine and Pase, Luke and Ramos-Lopez, Carlos Fernando and
 Lieschke, Graham J. and Renshaw, Stephen A. and Reyes-Aldasoro, Constantino Carlos},
 issn = {19326203},
 journal = {PLOS ONE},
 month = {January},
 number = {8},
 pages = {e72636},
 pmid = {24023630},
 title = {{PhagoSight: An Open-Source MATLAB\textsuperscript{\textregistered}\
 Package for the Analysis of
 Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model}},
 volume = {8},
 year = {2013}
}