1 Introduction

This document offers an introduction and overview of the R/Bioconductor (R Core Team 2014, Gentleman et al. (2004)) package flowcatchR, which provides a flexible and comprehensive set of tools to detect and track flowing blood cells in time-lapse microscopy.

2 Getting started

source("http://bioconductor.org/biocLite.R")
biocLite("flowcatchR")

install.packages("devtools") # if needed
devtools::install_github("federicomarini/flowcatchR")

maintainer("flowcatchR")

## [1] "Federico Marini <marinif@uni-mainz.de>"

citation("flowcatchR")

## 
## To cite package 'flowcatchR' in publications use:
## 
##   Federico Marini (2018). flowcatchR: Tools to analyze in vivo
##   microscopy imaging data focused on tracking flowing blood cells. R
##   package version 1.14.0.
##   https://github.com/federicomarini/flowcatchR
## 
## A BibTeX entry for LaTeX users is
## 
##   @Manual{,
##     title = {flowcatchR: Tools to analyze in vivo microscopy imaging data focused on
## tracking flowing blood cells},
##     author = {Federico Marini},
##     year = {2018},
##     note = {R package version 1.14.0},
##     url = {https://github.com/federicomarini/flowcatchR},
##   }

3 Processing overview

flowcatchR works primarily with sets of fluorescent time-lapse images, where the particles of interest are marked with a fluorescent label (e.g., red for blood platelets, green for leukocytes). Although different entry spots are provided (such as the coordinates of identified points in each frame via tab delimited files), we will illustrate the characteristics of the package starting from the common protocol starting point. In this case, we have a set of 20 frames derived from an intravital microscopy acquisition, which for the sake of practicality were already registered to reduce the unwanted specimen movements (Fiji (Schindelin, Arganda-Carreras, and Frise 2012) was used for this purpose).

library("flowcatchR")

## Loading required package: EBImage

data("MesenteriumSubset")

# printing summary information for the MesenteriumSubset object
MesenteriumSubset

## Frames 
##   colorMode    : Color 
##   storage.mode : double 
##   dim          : 271 131 3 20 
##   frames.total : 60 
##   frames.render: 20 
## 
## imageData(object)[1:5,1:6,1,1]
##           [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
## [1,] 0.1647059 0.2117647 0.1882353 0.1803922 0.1607843 0.1333333
## [2,] 0.2352941 0.1882353 0.1803922 0.1568627 0.1411765 0.1372549
## [3,] 0.2352941 0.2000000 0.1764706 0.1490196 0.1333333 0.1333333
## [4,] 0.2352941 0.2117647 0.1764706 0.1529412 0.1411765 0.1411765
## [5,] 0.2313725 0.2078431 0.1725490 0.1411765 0.1294118 0.1411765
## 
## Channel(s): all

To obtain the set of trajectories identified from the analysis of the loaded frames, a very compact one-line command is all that is needed:

# one command to seize them all :)
fullResults <- kinematics(trajectories(particles(channel.Frames(MesenteriumSubset,"red"))))

On a MAC OS X machine equipped with 2.8 Ghz Intel Core i7 processor and 16 GB RAM, the execution of this command takes 2.32 seconds to run (tests performed with the R package microbenchmark. On a more recent MacBook Pro (2017), the same benchmark took 1.78 seconds.

The following sections will provide additional details to the operations mentioned above, with more also on the auxiliary functions that are available in flowcatchR.

4 Image acquisition

A set of images is acquired, after a proper microscopy setup has been performed. This includes for example a careful choice of spatial and temporal resolution; often a compromise must be met to have a good frame rate and a good SNR to detect the particles in the single frames. For a good review on the steps to be taken, please refer to Meijering’s work (Meijering and Smal 2008, Meijering, Dzyubachyk, and Smal (2012)).

flowcatchR provides an S4 class that can store the information of a complete acquisition, namely Frames. The Frames class extends the Image class, defined in the EBImage package, and thus exploits the multi-dimensional array structures of the class. The locations of the images are stored as dimnames of the Frames object. To construct a Frames object from a set of images, the read.Frames function is used:

# initialization
fullData <- read.Frames(image.files="/path/to/folder/containing/images/", nframes=100) 
# printing summary information for the Frames object
fullData

nframes specifies the number of frames that will constitute the Frames object, whereas image.files is a vector of character strings with the full location of the (raw) images, or the path to the folder containing them (works automatically if images are in TIFF/JPG/PNG format). In this case we just loaded the full dataset, but for the demonstrational purpose of this vignette, we will proceed with the subset available in the MesenteriumSubset object, which we previously loaded in Section 3.

It is possible to inspect the images composing a Frames object with the function inspect.Frames (Fig. 1).

inspect.Frames(MesenteriumSubset, nframes=9, display.method="raster")

Figure 1: The first 9 frames of the MesenteriumSubset dataset
The red channel stores information about platelets, while the green channel is dedicated to leukocytes

By default, display.method is set to browser, as in the EBImage function display. This opens up a window in the predefined browser (e.g. Mozilla Firefox), with navigable frames (arrows on the top left corner). For the vignette, we will set it to raster, for viewing them as raster graphics using R’s native functions.

Importantly, these image sets were already registered and rotated in such a way that the overall direction of the movement of interest flows from left to right, as a visual aid and also to fit with some assumptions that will be done in the subsequent step of particle tracking. To register the images, we recommend the general purpose tools offered by suites such as ImageJ/Fiji (Schneider, Rasband, and Eliceiri 2012, Schindelin, Arganda-Carreras, and Frise (2012)).

For the following steps, we will focus on the information contained in the red channel, corresponding in this case to blood platelets. We do so by calling the channel.Frames function:

plateletsMesenterium <- channel.Frames(MesenteriumSubset, mode="red")
plateletsMesenterium

## Frames 
##   colorMode    : Grayscale 
##   storage.mode : double 
##   dim          : 271 131 20 
##   frames.total : 20 
##   frames.render: 20 
## 
## imageData(object)[1:5,1:6,1]
##           [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
## [1,] 0.1647059 0.2117647 0.1882353 0.1803922 0.1607843 0.1333333
## [2,] 0.2352941 0.1882353 0.1803922 0.1568627 0.1411765 0.1372549
## [3,] 0.2352941 0.2000000 0.1764706 0.1490196 0.1333333 0.1333333
## [4,] 0.2352941 0.2117647 0.1764706 0.1529412 0.1411765 0.1411765
## [5,] 0.2313725 0.2078431 0.1725490 0.1411765 0.1294118 0.1411765
## 
## Channel(s): red

This creates another instance of the class Frames, and we inspect it in its first 9 frames (Fig.2).

inspect.Frames(plateletsMesenterium, nframes=9, display.method="raster")

Figure 2: The first 9 frames for the red channel of the MesenteriumSubset dataset
This is just displaying the GrayScale signal for the red channel stored in plateletsMesenterium (for the thrombocytes)

5 Image preprocessing and analysis

Steps such as denoising, smoothing and morphological operations (erosion/dilation, opening/closing) can be performed thanks to the general functions provided by EBImage. flowcatchR offers a wrapper around a series of operations to be applied to all images in a Frames object. The function preprocess.Frames is called via the following command:

preprocessedPlatelets <- preprocess.Frames(plateletsMesenterium,
                                    brush.size=3, brush.shape="disc",
                                    at.offset=0.15, at.wwidth=10, at.wheight=10,
                                    kern.size=3, kern.shape="disc",
                                    ws.tolerance=1, ws.radius=1)
preprocessedPlatelets

## Frames 
##   colorMode    : Grayscale 
##   storage.mode : integer 
##   dim          : 271 131 20 
##   frames.total : 20 
##   frames.render: 20 
## 
## imageData(object)[1:5,1:6,1]
##      [,1] [,2] [,3] [,4] [,5] [,6]
## [1,]    0    0    0    0    0    0
## [2,]    0    0    0    0    0    0
## [3,]    0    0    0    0    0    0
## [4,]    0    0    0    0    0    0
## [5,]    0    0    0    0    0    0
## 
## Channel(s): red

The result of this is displayed in Fig.3. For a detailed explanation of the parameters to better tweak the performances of this segmentation step, please refer to the help of preprocess.Frames. To obtain an immediate feedback about the effects of the operations performed in the full preprocessing phase, we can call again inspect.Frames on the Frames of segmented images (Fig.3.

inspect.Frames(preprocessedPlatelets, nframes=9, display.method="raster")

Figure 3: The first 9 frames after preprocessing of the MesenteriumSubset dataset
The binarized image shows the detected objects after thresholding.

The frames could be cropped, if e.g. it is needed to remove background noise that might be present close to the edges. This is done with the function crop.Frames.

croppedFrames <- crop.Frames(plateletsMesenterium,
                     cutLeft=6, cutRight=6,
                     cutUp=3, cutDown=3,
                     testing=FALSE)
croppedFrames

## Frames 
##   colorMode    : Grayscale 
##   storage.mode : double 
##   dim          : 260 126 20 
##   frames.total : 20 
##   frames.render: 20 
## 
## imageData(object)[1:5,1:6,1]
##           [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
## [1,] 0.1803922 0.1568627 0.1372549 0.1372549 0.1333333 0.1176471
## [2,] 0.2039216 0.1843137 0.1490196 0.1254902 0.1215686 0.1215686
## [3,] 0.1843137 0.1764706 0.1568627 0.1294118 0.1176471 0.1019608
## [4,] 0.1921569 0.1568627 0.1529412 0.1333333 0.1254902 0.1333333
## [5,] 0.2000000 0.1647059 0.1490196 0.1450980 0.1333333 0.1411765
## 
## Channel(s): red

If testing is set to true, the function just displays the first cropped frame, to get a feeling whether the choice of parameters was adequate. Similarly, for the function rotate.Frames the same behaviour is expected, whereas the rotation in degrees is specified by the parameter angle.

rotatedFrames <- rotate.Frames(plateletsMesenterium, angle=30)
rotatedFrames

## Frames 
##   colorMode    : Grayscale 
##   storage.mode : double 
##   dim          : 300 249 20 
##   frames.total : 20 
##   frames.render: 20 
## 
## imageData(object)[1:5,1:6,1]
##      [,1] [,2] [,3] [,4] [,5] [,6]
## [1,]    0    0    0    0    0    0
## [2,]    0    0    0    0    0    0
## [3,]    0    0    0    0    0    0
## [4,]    0    0    0    0    0    0
## [5,]    0    0    0    0    0    0
## 
## Channel(s): red

If desired, it is possible to select just a subset of the frames belonging to a Frames. This can be done via the select.Frames function:

subsetFrames <- select.Frames(plateletsMesenterium,
                       framesToKeep=c(1:10,14:20))
subsetFrames

## Frames 
##   colorMode    : Grayscale 
##   storage.mode : double 
##   dim          : 271 131 17 
##   frames.total : 17 
##   frames.render: 17 
## 
## imageData(object)[1:5,1:6,1]
##           [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
## [1,] 0.1647059 0.2117647 0.1882353 0.1803922 0.1607843 0.1333333
## [2,] 0.2352941 0.1882353 0.1803922 0.1568627 0.1411765 0.1372549
## [3,] 0.2352941 0.2000000 0.1764706 0.1490196 0.1333333 0.1333333
## [4,] 0.2352941 0.2117647 0.1764706 0.1529412 0.1411765 0.1411765
## [5,] 0.2313725 0.2078431 0.1725490 0.1411765 0.1294118 0.1411765
## 
## Channel(s): red

If required, the user can decide to perform a normalization step (via normalizeFrames), to correct for systematic variations in the acquisition conditions, in case the overall intensity levels change, e.g., when the acquisition spans long time scales. In this case, the median of the intensity sums is chosen as a scaling factor.

normFrames <- normalizeFrames(plateletsMesenterium,normFun = "median")

The user can choose any combination of the operations in order to segment the images provided as input, but preprocess.Frames is a very convenient high level function for proceeding in the workflow. It is also possible, as it was shown in the introductory one-liner, to call just particles on the raw Frames object. In this latter case, particles computes the preprocessed Frames object according to default parameters. Still, in either situation, the output for this step is an object of the ParticleSet class.

platelets <- particles(plateletsMesenterium, preprocessedPlatelets)

## Computing features in parallel...
## Done!

platelets

## An object of the ParticleSet class. 
## 
## Set of particles for 20 images
## 
## Displaying a subset of the features of the 13 particles found in the first image...
##   cell.0.m.cx cell.0.m.cy cell.0.m.majoraxis cell.0.m.eccentricity
## 1   186.70833   47.937500           8.916405             0.6353715
## 2   256.19048   35.857143           7.746554             0.4606665
## 3   251.09524   63.523810           8.552466             0.6843186
## 4   215.54688   51.828125          13.694783             0.8788344
## 5    15.82759    8.517241           7.548790             0.7570114
##   cell.0.m.theta cell.0.s.area cell.0.s.perimeter cell.0.s.radius.mean
## 1      0.3380463            48                 20             3.487042
## 2      0.9165252            42                 19             3.194559
## 3      0.9370618            42                 19             3.247531
## 4      0.7172299            64                 28             4.308530
## 5      1.5439842            29                 16             2.622403
## 
## Particles identified on the red channel

The function particles leverages on the multi-core architecture of the systems where the analysis is run, and this is implemented via BiocParallel (updated since Version 1.0.3).

As it can be seen from the summary information, each ParticleSet stores the essential information on all particles that were detected in the original images, alongside with a complete set of features, which are computed by integrating the information from both the raw and the segmented frames.

A ParticleSet can be seen as a named list, where each element is a data.frame for a single frame, and the image source is stored as names to help backtracking the operations performed, and the slot channel is retained as selected in the initial steps.

It is possible to filter out particles according to their properties, such as area, shape and eccentricity. This is possible with the function select.particles. The current implementation regards only the surface extension, but any additional feature can be chosen and adopted to restrict the number of candidate particles according to particular properties which are expected and/or to remove potential noise that went through the preprocessing phase.

selectedPlatelets <- select.particles(platelets, min.area=3)

## Filtering the particles...

selectedPlatelets

## An object of the ParticleSet class. 
## 
## Set of particles for 20 images
## 
## Displaying a subset of the features of the 13 particles found in the first image...
##   cell.0.m.cx cell.0.m.cy cell.0.m.majoraxis cell.0.m.eccentricity
## 1   186.70833   47.937500           8.916405             0.6353715
## 2   256.19048   35.857143           7.746554             0.4606665
## 3   251.09524   63.523810           8.552466             0.6843186
## 4   215.54688   51.828125          13.694783             0.8788344
## 5    15.82759    8.517241           7.548790             0.7570114
##   cell.0.m.theta cell.0.s.area cell.0.s.perimeter cell.0.s.radius.mean
## 1      0.3380463            48                 20             3.487042
## 2      0.9165252            42                 19             3.194559
## 3      0.9370618            42                 19             3.247531
## 4      0.7172299            64                 28             4.308530
## 5      1.5439842            29                 16             2.622403
## 
## Particles identified on the red channel

This step can be done iteratively, with the help of the function add.contours. If called with the parameter mode set to particles, then it will automatically generate a Frames object, with the contours of all particles drawn around the objects that passed the segmentation (and filtering) step (Fig.4).

paintedPlatelets <- add.contours(raw.frames=MesenteriumSubset,
                                 binary.frames=preprocessedPlatelets,
                                 mode="particles")
inspect.Frames(paintedPlatelets, nframes=9, display.method="raster")

Figure 4: Particles detected in the first 9 frames
Particles detected in the first 9 frames are shown in yellow, with their contours defined by the segmentation procedure.

To connect the particles from one frame to the other, we perform first the detection of particles on all images. Only in a successive phase, we establish the links between the so identified objects. This topic will be covered in detail in the following section.

6 Particle tracking

To establish the connections between particles, the function to be called is link.particles. The algorithm used to perform the tracking itself is an improved version of the original implementation of Sbalzarini and Koumotsakos (Sbalzarini and Koumoutsakos 2005). To summarize the method, it is a fast and efficient self-initializing feature point tracking algorithm (using the centroids of the objects as reference) (Chenouard et al. 2014). The initial version is based on a particle matching algorithm, approached via a graph theory technique. It allows for appearances/disappearances of particles from the field of view, also temporarily as it happens in case of occlusions and objects leaving the plane of focus.

Our implementation adds to the existing one by redefining the cost function used in the optimization phase of the link assignment. It namely adds two terms, such as intensity variation and area variation, and mostly important implements a function to penalize the movements that are either perpendicular or backwards with respect to the oriented flow of cells. Small unwanted movements, which may be present even after the registration phase, are handled with two jitter terms in a defined penalty function. Multiplicative factors can further influence the penalties given to each term.

In its default value, the penalty function is created via the penaltyFunctionGenerator. The user can exploit the parameter values in it to create a custom version of it, to match the particular needs stemming from the nature of the available data and phenomenon under inspection.

defaultPenalty <- penaltyFunctionGenerator()
print(defaultPenalty)

## function (angle, distance) 
## {
##     lambda1 * (distance/(1 - lambda2 * (abs(angle)/(pi + epsilon1))))
## }
## <bytecode: 0x000000000df75a98>
## <environment: 0x000000000df76cc0>

As mentioned above, to perform the linking of the particles, we use link.particles. Fundamental parameters are L and R, named as in the original implementation. L is the maximum displacement in pixels that a particle is expected to have in two consecutive frames, and R is the value for the link range, i.e. the number of future frames to be considered for the linking (typically assumes values between 1 - when no occlusions are known to happen - and 3). An extended explanation of the parameters is in the documentation of the package.

linkedPlatelets <- link.particles(platelets,  
                                  L=26, R=3,
                                  epsilon1=0, epsilon2=0,
                                  lambda1=1, lambda2=0,
                                  penaltyFunction=penaltyFunctionGenerator(),
                                  include.area=FALSE)
linkedPlatelets

## An object of the LinkedParticleSet class. 
## 
## Set of particles for 20 images
## 
## Particles are tracked throughout the subsequent 3 frame(s)
## 
## Displaying a subset of the features of the 13 particles found in the first image...
##   cell.0.m.cx cell.0.m.cy cell.0.m.majoraxis cell.0.m.eccentricity
## 1   186.70833   47.937500           8.916405             0.6353715
## 2   256.19048   35.857143           7.746554             0.4606665
## 3   251.09524   63.523810           8.552466             0.6843186
## 4   215.54688   51.828125          13.694783             0.8788344
## 5    15.82759    8.517241           7.548790             0.7570114
##   cell.0.m.theta cell.0.s.area cell.0.s.perimeter cell.0.s.radius.mean
## 1      0.3380463            48                 20             3.487042
## 2      0.9165252            42                 19             3.194559
## 3      0.9370618            42                 19             3.247531
## 4      0.7172299            64                 28             4.308530
## 5      1.5439842            29                 16             2.622403
## 
## Particles identified on the red channel

As it can be seen, linkedPlatelets is an object of the LinkedParticleSet class, which is a subclass of the ParticleSet class.

After inspecting the trajectories (see Section 7) it might be possible to filter a LinkedParticleSet class object and subsequently reperform the linking on its updated version (e.g. some detected particles were found to be noise, and thus removed with select.particles).

flowcatchR provides functions to export and import the identified particles, in order to offer an additional entry point for tracking and analyzing the trajectories (if particles were detected with other routines) and also to store separately the information per each frame about the objects that were primarily identified.

An example is provided in the lines below, with the functions export.particles and read.particles :

# export to csv format
export.particles(platelets, dir="/path/to/export/folder/exportParticleSet/")
# re-import the previously exported, in this case
importedPlatelets <- read.particles(particle.files="/path/to/export/folder/exportParticleSet/")

7 Trajectory analysis

It is possible to extract the trajectories with the correspondent trajectories function:

trajPlatelets <- trajectories(linkedPlatelets)

## Generating trajectories...

trajPlatelets

## An object of the TrajectorySet class. 
## 
## TrajectorySet composed of 20 trajectories
## 
## Trajectories cover a range of 20 frames
## Displaying a segment of the first trajectory...
##        xCoord   yCoord trajLabel frame frameobjectID
## 1_1  186.7083 47.93750         1     1             1
## 1_2  186.9649 48.26316         1     2             4
## 1_3  186.8136 48.18644         1     3             2
## 1_4  186.2807 47.70175         1     4             1
## 1_5  186.6897 47.87931         1     5             2
## 1_6  186.8269 48.11538         1     6             2
## 1_7  186.9643 48.30357         1     7             1
## 1_8  186.6207 48.36207         1     8             3
## 1_9  186.3273 48.05455         1     9             3
## 1_10 186.9821 48.19643         1    10             3
## 
## Trajectories are related to particles identified on the red channel

A TrajectorySet object is returned in this case. It consists of a two level list for each trajectory, reporting the trajectory as a data.frame, the number of points npoints (often coinciding with the number of nframes, when no gaps ngaps are present) and its ID. A keep flag is used for subsequent user evaluation purposes.

Before proceeding with the actual analysis of the trajectories, it is recommended to evaluate them by visual inspection. flowcatchR provides two complementary methods to do this, either plotting them (plot or plot2D.TrajectorySet) or drawing the contours of the points on the original image (add.contours).

By plotting all trajectories in a 2D+time representation, it’s possible to have an overview of all trajectories.

The following command gives an interactive 3D (2D+time) view of all trajectories (Fig.5):

plot(trajPlatelets, MesenteriumSubset)

The plot2D.TrajectorySet focuses on additional information and a different “point of view”, but can just display a two dimensional projection of the identified trajectories (Fig.6).

plot2D.TrajectorySet(trajPlatelets, MesenteriumSubset)

Figure 6: A 2D “flat” representation of the trajectories
This is more suitable to give an indication of the global movement

To have more insights on single trajectories, or on a subset of them, add.contours offers an additional mode called trajectories. Particles are drawn on the raw images with colours corresponding to the trajectory IDs. add.contours plots by default all trajectories, but the user can supply a vector of the IDs of interest to override this behaviour.

paintedTrajectories <- add.contours(raw.frames=MesenteriumSubset,
                                    binary.frames=preprocessedPlatelets,  
                                    trajectoryset=trajPlatelets,
                                    mode="trajectories")
paintedTrajectories

## Frames 
##   colorMode    : Color 
##   storage.mode : double 
##   dim          : 271 131 3 20 
##   frames.total : 60 
##   frames.render: 20 
## 
## imageData(object)[1:5,1:6,1,1]
##           [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
## [1,] 0.1647059 0.2117647 0.1882353 0.1803922 0.1607843 0.1333333
## [2,] 0.2352941 0.1882353 0.1803922 0.1568627 0.1411765 0.1372549
## [3,] 0.2352941 0.2000000 0.1764706 0.1490196 0.1333333 0.1333333
## [4,] 0.2352941 0.2117647 0.1764706 0.1529412 0.1411765 0.1411765
## [5,] 0.2313725 0.2078431 0.1725490 0.1411765 0.1294118 0.1411765
## 
## Channel(s): all

As with any other Frames object, it is recommended to take a peek at it via the inspect.Frames function (Fig.7):

inspect.Frames(paintedTrajectories,nframes=9,display.method="raster")

Figure 7: Particles detected in the first 9 frames
These are shown this time in colours corresponding to the identified trajectories, again with their contours defined by the segmentation procedure.

To allow for a thorough evaluation of the single trajectories, export.Frames is a valid helper, as it creates single images corresponding to each frame in the Frames object. We first extract for example trajectory 11 (Fig.8) with the following command:

traj11 <- add.contours(raw.frames=MesenteriumSubset,
                       binary.frames=preprocessedPlatelets,
                       trajectoryset=trajPlatelets,
                       mode="trajectories",
                       trajIDs=11)
traj11

## Frames 
##   colorMode    : Color 
##   storage.mode : double 
##   dim          : 271 131 3 20 
##   frames.total : 60 
##   frames.render: 20 
## 
## imageData(object)[1:5,1:6,1,1]
##           [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
## [1,] 0.1647059 0.2117647 0.1882353 0.1803922 0.1607843 0.1333333
## [2,] 0.2352941 0.1882353 0.1803922 0.1568627 0.1411765 0.1372549
## [3,] 0.2352941 0.2000000 0.1764706 0.1490196 0.1333333 0.1333333
## [4,] 0.2352941 0.2117647 0.1764706 0.1529412 0.1411765 0.1411765
## [5,] 0.2313725 0.2078431 0.1725490 0.1411765 0.1294118 0.1411765
## 
## Channel(s): all

inspect.Frames(traj11, nframes=9, display.method="raster")

Figure 8: First 9 frames for trajectory with ID 11
This is supplied to the trajIds argument of add.contours

The data for trajectory 11 in the TrajectorySet object can be printed to the terminal:

trajPlatelets[[11]]

## $trajectory
##         xCoord   yCoord trajLabel frame frameobjectID
## 11_1  186.5385 13.84615        11     1            11
## 11_2  186.5000 14.81250        11     2            12
## 11_3  186.4737 14.63158        11     3            11
## 11_4  186.0455 14.45455        11     4             9
## 11_5  186.5000 14.77778        11     5            11
## 11_6  186.5714 15.19048        11     6            12
## 11_7  186.7143 15.42857        11     7            11
## 11_8  186.4286 15.38095        11     8            12
## 11_9  186.0952 15.09524        11     9            11
## 11_10 186.6500 15.30000        11    10            13
## 11_11 186.5714 15.61905        11    11            14
## 11_12 186.7368 15.52632        11    12            12
## 11_13 186.8947 16.05263        11    13            12
## 11_14 186.5000 15.50000        11    14            15
## 11_15 186.8182 15.72727        11    15            13
## 11_16 186.9048 15.95238        11    16            11
## 11_17 186.8636 16.09091        11    17            12
## 11_18 187.0000 16.13636        11    18            11
## 11_19 186.6818 16.13636        11    19            15
## 11_20 186.5789 15.89474        11    20            16
## 
## $npoints
## [1] 20
## 
## $nframes
## [1] 20
## 
## $ngaps
## [1] 0
## 
## $keep
## [1] NA
## 
## $ID
## [1] 11

After that, it can also be exported with the following command (the dir parameter must be changed accordingly):

export.Frames(traj11, dir=tempdir(), nameStub="vignetteTest_traj11",
              createGif=TRUE, removeAfterCreatingGif=FALSE)

export.Frames offers multiple ways to export - animated gif (if ImageMagick is available and installed on the system) or multiple jpeg/png images.

Of course the user might want to singularly evaluate each trajectory that was identified, and this can be done by looping over the trajectory IDs.

evaluatedTrajectories <- trajPlatelets

for(i in 1:length(trajPlatelets))
{
  paintedTraj <- add.contours(raw.frames=MesenteriumSubset,
                              binary.frames=preprocessedPlatelets,
                              trajectoryset=trajPlatelets,
                              mode="trajectories",
                              col="yellow",
                              trajIDs=i)  
  export.Frames(paintedTraj,
                nameStub=paste0("vignetteTest_evaluation_traj_oneByOne_",i),
                createGif=TRUE, removeAfterCreatingGif=TRUE)
  ### uncomment the code below to perform the interactive evaluation of the single trajectories

  #   cat("Should I keep this trajectory? --- 0: NO, 1:YES --- no other values allowed")
  #   userInput <- readLines(n=1L)
  #   ## if neither 0 nor 1, do not update
  #   ## otherwise, this becomes the value for the field keep in the new TrajectoryList
  #   evaluatedTrajectories@.Data[[i]]$keep <- as.logical(as.numeric(userInput))
}

Always using trajectory 11 as example, we would set evaluatedTrajectories[[11]]$keep to TRUE, since the trajectory was correctly identified, as we just checked.

Once all trajectories have been selected, we can proceed to calculate (a set of) kinematic parameters, for a single or all trajectories in a TrajectorySet object. The function kinematics returns the desired output, respectively a KinematicsFeatures object, a KinematicsFeaturesSet, a single value or a vector (or list, if not coercible to vector) of these single values (one parameter for each trajectory).

allKinematicFeats.allPlatelets <- kinematics(trajPlatelets,
                                             trajectoryIDs=NULL, # will select all trajectory IDs 
                                             acquisitionFrequency=30, # value in milliseconds
                                             scala=50, # 1 pixel is equivalent to ... micrometer
                                             feature=NULL) # all kinematic features available

## Warning in extractKinematics.traj(trajectoryset, i, acquisitionFrequency =
## acquisitionFrequency, : The trajectory with ID 17 had 3 or less points, no
## features were computed.

## Warning in extractKinematics.traj(trajectoryset, i, acquisitionFrequency =
## acquisitionFrequency, : The trajectory with ID 18 had 3 or less points, no
## features were computed.

## Warning in extractKinematics.traj(trajectoryset, i, acquisitionFrequency =
## acquisitionFrequency, : The trajectory with ID 20 had 3 or less points, no
## features were computed.

As it is reported from the output, the function raises a warning for trajectories which have 3 or less points, as they might be spurious detections. In such cases, no kinematic features are computed.

allKinematicFeats.allPlatelets

## An object of the KinematicsFeaturesSet class. 
## 
## KinematicsFeaturesSet composed of 20  KinematicsFeatures objects
## 
## Available features (shown for the first trajectory):
##  [1] "delta.x"                     "delta.t"                    
##  [3] "delta.v"                     "totalTime"                  
##  [5] "totalDistance"               "distStartToEnd"             
##  [7] "curvilinearVelocity"         "straightLineVelocity"       
##  [9] "linearityForwardProgression" "trajMSD"                    
## [11] "velocityAutoCorr"            "instAngle"                  
## [13] "directChange"                "dirAutoCorr"                
## [15] "paramsNotComputed"          
## 
## Curvilinear Velocity: 0.009970094 
## Total Distance: 5.682953 
## Total Time: 570 
## 
## Average values (calculated on 3 trajectories where parameters were computed)
## Average Curvilinear Velocity: 0.1278174 
## Average Total Distance: 56.08449 
## Average Total Time: 518.8235

A summary for the returned object (in this case a KinematicsFeaturesSet) shows some of the computed parameters. By default, information about the first trajectory is reported in brief, and the same parameters are evaluated on average across the selected trajectories. The true values can be accessed in this case for each trajectory by the subset operator for lists ([[]]), followed by the name of the kinematic feature (e.g., $totalDistance).

A list of all available parameters is printed with an error message if the user specifies an incorrect name, such as here:

allKinematicFeats.allPlatelets <- kinematics(trajPlatelets, feature="?")

## Available features to compute are listed here below.
##           Please select one among delta.x, delta.t, delta.v, totalTime,
##           totalDistance, distStartToEnd, curvilinearVelocity,
##           straightLineVelocity, linearityForwardProgression, trajMSD,
##           velocityAutoCorr, instAngle, directChange or dirAutoCorr

When asking for a single parameter, the value returned is structured in a vector, such that it is straightforward to proceed with further analysis, e.g. by plotting the distribution of the curvilinear velocities (Fig.9).

allVelocities <- kinematics(trajPlatelets, feature="curvilinearVelocity")

hist(allVelocities, breaks=10, probability=TRUE, col="cadetblue",
     xlab="Curvilinear Velocities Distribution",
     main="Trajectory Analysis: Curvilinear Velocities")
lines(density(allVelocities, na.rm=TRUE), col="steelblue", lwd=2)

Figure 9: Histogram of the curvilinear velocities for all trajectories identified in the MesenteriumSubset dataset

For this code chunk, we are suppressing the warning messages, as they would be exactly the same as in the former where all features were computed for each trajectory.

8 Interactive tools for a user-friendly workflow solution

To enhance the Frames objects and deliver an immediate feedback to the user, the function snap leverages on both the raw and binary Frames, as well as on the corresponding ParticleSet and TrajectorySet objects. It integrates the information available in all the mentioned objects, and it plots a modified instance of the Frames object, identifying the particles closest to the mouse click, and showing additional trajectory-related information, such as the trajectory ID and the instantaneous velocity of the cell. The function can be called as in the command below:

snap(MesenteriumSubset,preprocessedPlatelets,
     platelets,trajPlatelets,
     frameID = 1,showVelocity = T)

An example output for the snap is shown below in Fig.10, where the information (trajectory ID, as well as the velocity in the selected frame) is shown in yellow to offer a good contrast with the fluorescent image.

Figure 10: Output generated by the snap function
The user wanted to identify the particle and additionally display the trajectory information (ID, instantaneous velocity) on it.

shinyFlow()

list.files(system.file("extdata",package = "flowcatchR"),pattern = "*.ipynb")

## [1] "template_DetectionOfTransmigrationEvents.ipynb"
## [2] "template_flowcatchR_vignetteSummary.ipynb"

$ ipython notebook

9 flowcatchR in Docker containers

flowcatchR is now (as of September 2015) available also in Docker images that are the components of the dockerflow proposal (https://github.com/federicomarini/dockerflow). This includes:

• flowstudio - https://github.com/federicomarini/flowstudio, a command-line/IDE interface to RStudio where flowcatchR and its dependencies are preinstalled
• flowshiny - https://github.com/federicomarini/flowshiny a Shiny Server running the shinyFlow web application
• flowjupy - https://github.com/federicomarini/flowjupy, a Jupyter Notebook interface

These three images can be run simultaneously, provided the system where the containers are running supports the docker-compose tool. For more information on how to install the single components, please refer to their repositories.

10 Supplementary information

For more information on the method adapted for tracking cells, see Sbalzarini and Koumotsakos (2005) (Sbalzarini and Koumoutsakos 2005). For additional details regarding the functions of flowcatchR, please consult the documentation or write an email to marinif@uni-mainz.de.

Due to space limitations, the complete dataset for the acquired frames used in this vignette is not included as part of the flowcatchR package. If you would like to get access to it, you can write an email to marinif@uni-mainz.de.

11 Acknowledgements

This package was developed at the Institute of Medical Biostatistics, Epidemiology and Informatics at the University Medical Center, Mainz (Germany), with the financial support provided by the TRP-A15 Translational Research Project grant.

flowcatchR incorporates suggestions and feedback from the wet-lab biology units operating at the Center for Thrombosis and Hemostasis (CTH), in particular Sven Jäckel and Kerstin Jurk. Sven Jäckel also provided us with the sample acquisition which is available in this vignette.

We would like to thank the members of the Biostatistics division for valuable discussions, and additionally Isabella Zwiener for contributing to the first ideas on the project.