Team:Imperial College/Validation

From 2008.igem.org

(Difference between revisions)
m
 
(4 intermediate revisions not shown)
Line 1: Line 1:
{{Imperial/StartPage2}}
{{Imperial/StartPage2}}
-
==== Validating Tracking Software ====
+
 
 +
=== Validating Tracking Software ===
{{Imperial/Box2||
{{Imperial/Box2||
ImageJ was used primarily to analyse images. Various plugins were tested, such as SpotTracker and Particle Tracker, but both failed to producing any form of convincing result. Microscopy videos were captured using Volocity software, which also provided a cell tracking function. Thus analysis of synthetic videos was done '''manually''' and using 64-Bit '''Volocity''' analysis software. The synthetic video shown to the right was used as an input for the tracking of synthetic cells.  
ImageJ was used primarily to analyse images. Various plugins were tested, such as SpotTracker and Particle Tracker, but both failed to producing any form of convincing result. Microscopy videos were captured using Volocity software, which also provided a cell tracking function. Thus analysis of synthetic videos was done '''manually''' and using 64-Bit '''Volocity''' analysis software. The synthetic video shown to the right was used as an input for the tracking of synthetic cells.  
Line 39: Line 40:
*Manual Tracking
*Manual Tracking
-
{{{Pipe}} border{{Equals}}"1" cellpadding{{Equals}}"5" cellspacing{{Equals}}"0" align{{Equals}}"center"
+
{{{Pipe}} border{{Equals}}"0" cellpadding{{Equals}}"5" cellspacing{{Equals}}"0" align{{Equals}}"center" style{{Equals}}"background-color:transparent;color:#2B48B3;"
{{Pipe}}-
{{Pipe}}-
{{Pipe}}'''Error in X Coordinate'''
{{Pipe}}'''Error in X Coordinate'''
Line 47: Line 48:
{{Pipe}}[[Image:Multiple Error Y px.JPG{{Pipe}}250px]]
{{Pipe}}[[Image:Multiple Error Y px.JPG{{Pipe}}250px]]
{{Pipe}}-
{{Pipe}}-
-
{{Pipe}}Mean {{Equals}} 1.7354, Standard Deviation {{Equals}} 1.7187
+
{{Pipe}}Mean {{Equals}} 1.7354, <br>Standard Deviation {{Equals}} 1.7187
-
{{Pipe}}Mean {{Equals}} 1.2524, Standard Deviation {{Equals}} 1.0568
+
{{Pipe}}Mean {{Equals}} 1.2524, <br>Standard Deviation {{Equals}} 1.0568
{{Pipe}}-
{{Pipe}}-
{{Pipe}}'''Error in X Displacement'''
{{Pipe}}'''Error in X Displacement'''
Line 58: Line 59:
{{Pipe}}[[Image:Multiple_Error_Distance.JPG{{Pipe}}250px]]
{{Pipe}}[[Image:Multiple_Error_Distance.JPG{{Pipe}}250px]]
{{Pipe}}-
{{Pipe}}-
-
{{Pipe}}Mean {{Equals}} -0.0022, Standard Deviation {{Equals}} 1.0002
+
{{Pipe}}Mean {{Equals}} -0.0022, <br>Standard Deviation {{Equals}} 1.0002
-
{{Pipe}}Mean {{Equals}} -0.0018, Standard Deviation {{Equals}} 0.6795
+
{{Pipe}}Mean {{Equals}} -0.0018, <br>Standard Deviation {{Equals}} 0.6795
-
{{Pipe}}Mean {{Equals}} -0.1506, Standard Deviation {{Equals}} 0.9196
+
{{Pipe}}Mean {{Equals}} -0.1506, <br>Standard Deviation {{Equals}} 0.9196
{{Pipe}}-
{{Pipe}}-
{{Pipe}}}
{{Pipe}}}
Line 67: Line 68:
====== Volocity ======
====== Volocity ======
-
{{{Pipe}} border{{Equals}}"1" cellpadding{{Equals}}"5" cellspacing{{Equals}}"0" align{{Equals}}"center"
+
{{{Pipe}} border{{Equals}}"0" cellpadding{{Equals}}"5" cellspacing{{Equals}}"0" align{{Equals}}"center" style{{Equals}}"background-color:transparent;color:#2B48B3;"
{{Pipe}}-
{{Pipe}}-
{{Pipe}}'''Error in X Coordinate'''
{{Pipe}}'''Error in X Coordinate'''
Line 75: Line 76:
{{Pipe}}[[Image:Volocity Y Error.JPG{{Pipe}}250px]]
{{Pipe}}[[Image:Volocity Y Error.JPG{{Pipe}}250px]]
{{Pipe}}-
{{Pipe}}-
-
{{Pipe}}Mean {{Equals}} -1.7149, Standard Deviation {{Equals}} 0.1376
+
{{Pipe}}Mean {{Equals}} -1.7149, <br>Standard Deviation {{Equals}} 0.1376
-
{{Pipe}}Mean {{Equals}} -0.4907, Standard Deviation {{Equals}} 0.1614
+
{{Pipe}}Mean {{Equals}} -0.4907, <br>Standard Deviation {{Equals}} 0.1614
{{Pipe}}-
{{Pipe}}-
{{Pipe}}'''Error in X Displacement'''
{{Pipe}}'''Error in X Displacement'''
Line 86: Line 87:
{{Pipe}}[[Image:Volocity Distance Error.JPG{{Pipe}}250px]]
{{Pipe}}[[Image:Volocity Distance Error.JPG{{Pipe}}250px]]
{{Pipe}}-
{{Pipe}}-
-
{{Pipe}}Mean {{Equals}} 8.2732e-005, Standard Deviation {{Equals}} 0.1111
+
{{Pipe}}Mean {{Equals}} 8.2732e-005, <br>Standard Deviation {{Equals}} 0.1111
-
{{Pipe}}Mean {{Equals}} 6.1416e-004, Standard Deviation {{Equals}} 0.0712
+
{{Pipe}}Mean {{Equals}} 6.1416e-004, <br>Standard Deviation {{Equals}} 0.0712
-
{{Pipe}}Mean {{Equals}} 1.4262e-004, Standard Deviation {{Equals}} 0.0947
+
{{Pipe}}Mean {{Equals}} 1.4262e-004, <br>Standard Deviation {{Equals}} 0.0947
{{Pipe}}-
{{Pipe}}-
{{Pipe}}}
{{Pipe}}}
-
 
-
 
|}}
|}}
{{Imperial/Box1|Evaluation|
{{Imperial/Box1|Evaluation|
-
 
+
{{{Pipe}} border{{Equals}}"1px" cellpadding{{Equals}}"5" cellspacing{{Equals}}"0" align{{Equals}}"center" style{{Equals}}"background-color:transparent;color:#2B48B3;"
-
{{{Pipe}} border{{Equals}}"1" cellpadding{{Equals}}"5" cellspacing{{Equals}}"0" align{{Equals}}"center"
+
{{Pipe}}-
{{Pipe}}-
{{Pipe}}
{{Pipe}}
Line 113: Line 111:
{{Pipe}}}
{{Pipe}}}
-
|}}
 
-
*Manual tracking will be used to track ''B. subtilis''.
+
======Manual tracking will be used to track ''B. subtilis''.======
 +
|}}
{{Imperial/EndPage|Motility|Motility}}
{{Imperial/EndPage|Motility|Motility}}

Latest revision as of 02:56, 30 October 2008


Validating Tracking Software

ImageJ was used primarily to analyse images. Various plugins were tested, such as SpotTracker and Particle Tracker, but both failed to producing any form of convincing result. Microscopy videos were captured using Volocity software, which also provided a cell tracking function. Thus analysis of synthetic videos was done manually and using 64-Bit Volocity analysis software. The synthetic video shown to the right was used as an input for the tracking of synthetic cells.

Volocity

Volocity 64-Bit was used to analyse synthetic videos created. The following protocol was followed:

  1. Filter images using SD intensity of lower limit -100 and upper limit -35. This is to select cells which have a dark cell body.
  2. Set tracking method to trajectory variation
  3. Check the box "Ignore Stationary Objects" to disable tracking of the image border
  4. Set displacement estimation to automatic
  5. Begin tracking using Ctrl-U
Manual Tracking

Synthetic cells were tracked using ImageJ via the Manual Tracking Plugin. The following protocol was followed:

  1. Save .avi movie as an image sequence and then import image sequence.
  2. Start Manual Tracking Plugin.
  3. Identify the cell of interest and start new track.
  4. Click on the centroid of the cell of interest. This will cause the image to advance to the next frame. Continue till the cell exits field of view
  5. Once tracking is complete, end track and save results with a .xls extension.

Validation Process

A synthetic video of five cells with changing shape was used in the evaluation of tracking software. Each cell was tracked using respective tracking software, and their coordinates in pixels were obtained.

The following steps were taken to analyse tracking data:

  1. Convert synthetic trajectory coordinate points into pixels.
  2. Calculate the displacement in each frame for both synthetic and tracking data
  3. Calculate the distance travelled in each frame for both synthetic and tracking data
  4. Obtain the errors in coordinates, displacement and distance travelled by the cell

Results


The errors associated with manual tracking and Volocity software are shown below. All errors are given in terms of pixels.

  • Manual Tracking
Error in X Coordinate Error in Y Coordinate
Multiple Error X.JPG Multiple Error Y px.JPG
Mean = 1.7354,
Standard Deviation = 1.7187 		Mean = 1.2524,
Standard Deviation = 1.0568
Error in X Displacement Error in Y Displacement Error in Distance
Multiple Error X Displacement.JPG Multiple Error Y Displacement.JPG Multiple Error Distance.JPG
Mean = -0.0022,
Standard Deviation = 1.0002 		Mean = -0.0018,
Standard Deviation = 0.6795 		Mean = -0.1506,
Standard Deviation = 0.9196


Volocity
Error in X Coordinate Error in Y Coordinate
Volocity X Error.JPG Volocity Y Error.JPG
Mean = -1.7149,
Standard Deviation = 0.1376 		Mean = -0.4907,
Standard Deviation = 0.1614
Error in X Displacement Error in Y Displacement Error in Distance
Volocity X Displacement Error.JPG Volocity Y Displacement Error.JPG Volocity Distance Error.JPG
Mean = 8.2732e-005,
Standard Deviation = 0.1111 		Mean = 6.1416e-004,
Standard Deviation = 0.0712 		Mean = 1.4262e-004,
Standard Deviation = 0.0947

Evaluation
Volocity Manual Tracking
Pros Lower error in terms of tracking centroid than other tracking software.
Less time consuming. 		Able to discern cells visually.
Able track over larger number of frames.
Cons Failure to track cells continuously over a long number of frames > 70.
Biased to cells which run, rather than tumble.
Failure to discern motile from immotile or dead cells. 		Time consuming.
Higher error in terms of tracking centroid as compared to tracking software.


Manual tracking will be used to track B. subtilis.


Retrieved from "http://2008.igem.org/Team:Imperial_College/Validation"