WimTaxis
For Cell and Bacteria Tracking
Specifications for a successful analysis
Standard Tool
1
Description of WimTaxis ............................................................................................................. 2
2
Specifications for a successful analysis .................................................................................. 2
2.1 Upload requirements………………………………………………………………………………...2
2.2 Valid Formats ........................................................................................................................... 2
2.3 Characteristics of the input ................................................................................................ 2
2.4 Characteristics of the cell/bacterium culture ............................................................. 3
2.5 Characteristics of the frames/images………………………………………………………..3
2.6 Optional parameters of the analysis ............................................................................ …3
3
Results.................................................................................................................................................. 3
3.1 Order Summary....................................................................................................................... 3
3.2 Video Summary 1 ................................................................................................................... 4
Parameters of the Analysis ................................................................................................. 4
Start and end points ............................................................................................................... 4
Measurements.......................................................................................................................... 5
Track Activity............................................................................................................................ 6
Extra information about the tracks .................................................................................. 6
3.3 Video Summary 2 ................................................................................................................... 6
3.4 Tracking Results ..................................................................................................................... 7
Example and equations......................................................................................................... 7
3.5 Track Position Data ............................................................................................................... 8
3.6 Track Video ............................................................................................................................... 8
3.7 Chart Video ............................................................................................................................... 9
Wimasis GmbH | Karlstraße 55 | D-80333 Munich (Germany) | CEO Carlos Urquízar
© Copyright 2009 - 2013 Wimasis GmbH. All rights reserved.
Page 1 of 9
WimTaxis
For Cell and Bacteria Tracking
1 Description of WimTaxis
WimTaxis is specifically designed to detect and track cells and bacteria throughout a video in chemotaxis assay
and other similar assays. WimTaxis measures parameters related to the cell and bacterium trajectories, such as
the forward migration index, the displacement, the directionality and the velocity of the cell or bacterium.
WimTaxis standard tool is designed to work with many different cell and bacterium types, so it provides a
successful evaluation for a wide range of cells and bacteria. It is also adapted to work with images and videos
with different characteristics.
2
Specifications for a successful analysis
2.1 Upload requirements
WimTaxis only analyzes image time series. An image time series is a set of images of the same region that have
been taken at consecutive and equidistant times.
A series can be uploaded as a video/stack file or as a group of image files inside a folder. More than one series can
be uploaded in the same order. The maximum upload size is 1 GB per order.
2.2 Valid Formats
WimTaxis accepts the following file formats:
Images

jpg/jpeg
 jp2
 tif/tiff
Videos and Stacks

tif/tiff


mov
avi

png

wmv


gif
bmp

zvi

mpeg/mpg
In any case, low compression is strongly recommended in order to have high-quality images.
2.3 Characteristics of the input
•
Maximum number of frames per video/folder: 250. If more than 250 frames or images per folder are
uploaded, WimTaxis analyzes only the first 250 frames.
•
Minimum number of frames per video/folder: 10. If less than 10 frames or images per folder are uploaded,
WimTaxis does not analyze them.
•
Frames per second (fps) ratio
fps 
Velocityof CellorBact erium
CellorBact eriumDiameter
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© Copyright 2009 - 2013 Wimasis GmbH. All rights reserved.
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WimTaxis
For Cell and Bacteria Tracking
2.4 Characteristics of the cell/bacterium culture
•
Only one cell/bacterium phenotype.
•
Well-defined cell/bacterium border. Cells/bacteria should be easily distinguished from the background.
•
Low cell/bacterium division rate.
•
Low or medium density of cells/bacteria.
•
No clustering.
2.5 Characteristics of the frames/images
•
No additional information (e.g. scale bars, time stamp, etc.).
•
No vibration or displacement.
•
Focused.
•
No artifacts, noise or debris.
•
Homogeneous illumination.
2.6 Optional parameters of the analysis
The user can specify some parameters in order to get the results into different units:
•
Scale [µm/px]. If the user enters the µm/px conversion factor indicated in the microscope, the data readouts
will be given in µm instead of px.
•
Frames per second [frame/s]. If the user provides the frames/s, the velocity will be in seconds instead of
frames.
3
Results
Results are given in a zip file. Files included in the zip are:
1. Order Summary (one per order)
2. Video Summary 1 (one per uploaded video)
3. Video Summary 2 (one per uploaded video)
4. Tracking Results (one per uploaded video)
5. Track Position Data (one per uploaded video)
6. Track Video (one per uploaded video)
7. Chart Video (one per uploaded video)
3.1 Order Summary
It is a document with relevant important information of the order. It is a csv file, whose name is formed as follows
orderNum_Summary.csv. One Order Summary file per order is provided.
Wimasis GmbH | Karlstraße 55 | D-80333 Munich (Germany) | CEO Carlos Urquízar
© Copyright 2009 - 2013 Wimasis GmbH. All rights reserved.
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WimTaxis
For Cell and Bacteria Tracking
Illustration 3.1: Example of Order Summary
The information contained in the Order Summary file is: number of analyzed videos and their names. Remember that
more than one video per order can be uploaded in the same order and a file structure is allowed.
3.2 Video Summary 1
The Video Summary 1 is a document with the values of the parameters quantified by WimTaxis in the cell or
bacterium tracking assay. It is a csv file, whose name is composed as follows videoName_Summary.csv. One file is
provided per uploaded video.
Table 1: Example of Generic Track Information in Video Summary
The information in the Video Summary 1 is organized per Tracks. There is one row per each track. (Each track =
single bacteria movement throughout the video)
Parameters of the Analysis
The scale and frames per second parameters are shown in the first two rows of the document.
Start and end points
They are provided in [px] units and indicate the beginning and the end points of each track in the video.
•
xStart: x coordinate of the start point of the track.
•
xend: x coordinate of the end point of the track.
•
yStart: y coordinate of the start point of the track.
•
yend: y coordinate of the end point of the track.
Wimasis GmbH | Karlstraße 55 | D-80333 Munich (Germany) | CEO Carlos Urquízar
© Copyright 2009 - 2013 Wimasis GmbH. All rights reserved.
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WimTaxis
For Cell and Bacteria Tracking
Measurements1
(n = amount of detected tracks)
•
p-Value (Rayleigh Test for homogeneous distribution on the endpoints)[1]
Where:
•
Track Length: Accumulated distance of each track
Units : [um]
•
Displacement: Euclidean distance of each track
Units : [um]
Figure 1: Euclidean distance and accumulated distance
1
The measurements are calculated only for active tracks. The description of an active track can be found in page 8.
Wimasis GmbH | Karlstraße 55 | D-80333 Munich (Germany) | CEO Carlos Urquízar
© Copyright 2009 - 2013 Wimasis GmbH. All rights reserved.
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WimTaxis
For Cell and Bacteria Tracking
•
Average Velocity and Acceleration of each track
◦
velocity units : [um/sec]
◦
acceleration units: [um/sec²]
Track Activity
•
All Tracks: number of detected tracks along the video.
•
Active Tracks: number of tracks with significant movement. The significance is defined by the object radius
value. If the total movement of one track is bigger than its radius size, the track is considered in movement.
•
Non-Active Tracks: number of tracks with non-significant movement. If the total movement of one track is
less than its radius size, the track is considered still, so it will not be included in the measurements.
•
Activity Ratio: ratio between Active Tracks and All Tracks.
Extra information about the tracks
•
First Frame: frame in which the track first appears.
•
Last Frame: last image in which the track appears.
•
Total Frames: number of frames in which the track appears (Last Frame – First Frame + 1)
3.3 Video Summary 2
The Video Summary 2 is a document with the center of mass statistics provided per image analyzed. It is a csv file,
whose name is composed as follows videoName_Summary2.csv. One file is provided per uploaded video.
Table 2: Example of Video Summary 2
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© Copyright 2009 - 2013 Wimasis GmbH. All rights reserved.
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WimTaxis
For Cell and Bacteria Tracking
The information in the Video Summary 2 is organized per image analyzed. There is one row per image and each row
gives information about the position and measurements of the center of mass of the tracks in each frame.
The x and y coordinates are calculated using all normalized positions of all the tracks that were found in each frame
and all the tracks that finished before that frame (n). The normalization of the tracks means that all tracks are taken as
if starting at position (0,0).
The unit for the results is the [px] or [um], if specifically provided the µm/px conversion factor.
The position of the center of mass can be observed graphically in the chart video.
Directionality, Track Length, Displacement, Velocity, and Acceleration columns represents the evolution of these
parameters throughout the video and are always calculated using the center of mass positions from the frame 1
(starting position) to the corresponding frame (ending position). That is the reason why all parameters in the first
image have a value of 0, except for the directionality, whose first value is 1.
Track Length, Displacement, Velocity, and Acceleration have been calculated with the same equations used for
each track in Summary 1, but now the positions used are the center of mass positions instead of the track positions. As
there is only one center of mass, in this case n = 1.
3.4 Tracking Results
The Tracking Results file is a document with relevant information about the tracking. It is a txt file, whose name is
composed as follows videoName_results.txt. One file is provided per uploaded video2.
Example and equations
Slice length in dataset: from 1 to 100
Number of current used tracks: 112
% number of analyzed images
% n = number of tracks found
x Forward Migration Index: 0.0087299
%
y Forward Migration Index: -0.0031487
%
Directionality: 0.11108
%
Center of mass
x: 0.64909
%
y: -0.51521
%
Length: 0.82871
%
2
Read with MS Office or openOffice to see the data with a good format.
Wimasis GmbH | Karlstraße 55 | D-80333 Munich (Germany) | CEO Carlos Urquízar
© Copyright 2009 - 2013 Wimasis GmbH. All rights reserved.
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WimTaxis
For Cell and Bacteria Tracking
Accumulated distance
Max distance: 655.5076
Min distance: 13.8284
Mean distance: 127.3562 SD: 110.8234
%
Euclidean distance
Max distance: 83.728
Min distance: 0.20259
Mean distance: 10.5769 SD: 11.9418
%
3.5 Track Position Data
The Track Position Data is a document that contains information about the position of each track in each frame where
it appears. It is a xls file, whose name is formed as follows videoName_trackInfo.xls. One file is provided per
uploaded video.
This file has the same format as the track info file of ImageJ plug-in “Manual Tracking”, which means that it can be
used as input for this plug-in and get the charts, results, etc. provided by it. This way, WimTaxis results can be
compared and completed with the ImageJ plug-in results.
Table 3: Example of Track Position Data Chart
3.6 Track Video
The track video is a copy of the uploaded video with the trajectories of each tracked cell/bacterium drawn in different
colors and the ID of the track appointed. It is an avi file, whose name is formed as follows videoName_track.avi.
The different colors of the tracks do not have any meaning; they are randomly chosen to distinguish one track from
the others.
Wimasis GmbH | Karlstraße 55 | D-80333 Munich (Germany) | CEO Carlos Urquízar
© Copyright 2009 - 2013 Wimasis GmbH. All rights reserved.
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WimTaxis
For Cell and Bacteria Tracking
3.7 Chart Video
The chart video shows all the normalized trajectories in order to help observe better the tendency in the
directionality of the cell/bacterium culture. It is an avi file named as follows videoName_chart.avi.
The red spot is the center of mass of all normalized tracks and corresponds to the center of mass described in
the section 3.3.
Illustration 3.2: Example of chart video
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© Copyright 2009 - 2013 Wimasis GmbH. All rights reserved.
Page 9 of 9