Team:Imperial College/Validation
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=== 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. | ||
- | == Volocity == | + | ===== Volocity ===== |
Volocity 64-Bit was used to analyse synthetic videos created. The following protocol was followed: | Volocity 64-Bit was used to analyse synthetic videos created. The following protocol was followed: | ||
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#Begin tracking using Ctrl-U | #Begin tracking using Ctrl-U | ||
- | == Manual Tracking == | + | ===== Manual Tracking ===== |
Synthetic cells were tracked using ImageJ via the Manual Tracking Plugin. The following protocol was followed: | Synthetic cells were tracked using ImageJ via the Manual Tracking Plugin. The following protocol was followed: | ||
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The errors associated with manual tracking and Volocity software are shown below. All errors are given in terms of pixels. | The errors associated with manual tracking and Volocity software are shown below. All errors are given in terms of pixels. | ||
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*Manual Tracking | *Manual Tracking | ||
- | { | + | {{{Pipe}} border{{Equals}}"0" cellpadding{{Equals}}"5" cellspacing{{Equals}}"0" align{{Equals}}"center" style{{Equals}}"background-color:transparent;color:#2B48B3;" |
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- | + | {{Pipe}}'''Error in X Coordinate''' | |
- | + | {{Pipe}}'''Error in Y Coordinate''' | |
- | + | {{Pipe}}- | |
- | + | {{Pipe}}[[Image:Multiple Error X.JPG{{Pipe}}250px]] | |
- | + | {{Pipe}}[[Image:Multiple Error Y px.JPG{{Pipe}}250px]] | |
- | + | {{Pipe}}- | |
- | + | {{Pipe}}Mean {{Equals}} 1.7354, <br>Standard Deviation {{Equals}} 1.7187 | |
- | + | {{Pipe}}Mean {{Equals}} 1.2524, <br>Standard Deviation {{Equals}} 1.0568 | |
- | + | {{Pipe}}- | |
- | + | {{Pipe}}'''Error in X Displacement''' | |
- | + | {{Pipe}}'''Error in Y Displacement''' | |
- | + | {{Pipe}}'''Error in Distance''' | |
- | + | {{Pipe}}- | |
- | + | {{Pipe}}[[Image:Multiple Error X Displacement.JPG{{Pipe}}250px]] | |
- | + | {{Pipe}}[[Image:Multiple Error Y Displacement.JPG{{Pipe}}250px]] | |
- | + | {{Pipe}}[[Image:Multiple_Error_Distance.JPG{{Pipe}}250px]] | |
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- | + | {{Pipe}}Mean {{Equals}} -0.0022, <br>Standard Deviation {{Equals}} 1.0002 | |
- | + | {{Pipe}}Mean {{Equals}} -0.0018, <br>Standard Deviation {{Equals}} 0.6795 | |
- | + | {{Pipe}}Mean {{Equals}} -0.1506, <br>Standard Deviation {{Equals}} 0.9196 | |
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- | + | {{Pipe}}} | |
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- | + | ====== Volocity ====== | |
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+ | {{{Pipe}} border{{Equals}}"0" cellpadding{{Equals}}"5" cellspacing{{Equals}}"0" align{{Equals}}"center" style{{Equals}}"background-color:transparent;color:#2B48B3;" | ||
+ | {{Pipe}}- | ||
+ | {{Pipe}}'''Error in X Coordinate''' | ||
+ | {{Pipe}}'''Error in Y Coordinate''' | ||
+ | {{Pipe}}- | ||
+ | {{Pipe}}[[Image:Volocity X Error.JPG{{Pipe}}250px]] | ||
+ | {{Pipe}}[[Image:Volocity Y Error.JPG{{Pipe}}250px]] | ||
+ | {{Pipe}}- | ||
+ | {{Pipe}}Mean {{Equals}} -1.7149, <br>Standard Deviation {{Equals}} 0.1376 | ||
+ | {{Pipe}}Mean {{Equals}} -0.4907, <br>Standard Deviation {{Equals}} 0.1614 | ||
+ | {{Pipe}}- | ||
+ | {{Pipe}}'''Error in X Displacement''' | ||
+ | {{Pipe}}'''Error in Y Displacement''' | ||
+ | {{Pipe}}'''Error in Distance''' | ||
+ | {{Pipe}}- | ||
+ | {{Pipe}}[[Image:Volocity X Displacement Error.JPG{{Pipe}}250px]] | ||
+ | {{Pipe}}[[Image:Volocity Y Displacement Error.JPG{{Pipe}}250px]] | ||
+ | {{Pipe}}[[Image:Volocity Distance Error.JPG{{Pipe}}250px]] | ||
+ | {{Pipe}}- | ||
+ | {{Pipe}}Mean {{Equals}} 8.2732e-005, <br>Standard Deviation {{Equals}} 0.1111 | ||
+ | {{Pipe}}Mean {{Equals}} 6.1416e-004, <br>Standard Deviation {{Equals}} 0.0712 | ||
+ | {{Pipe}}Mean {{Equals}} 1.4262e-004, <br>Standard Deviation {{Equals}} 0.0947 | ||
+ | {{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}}- | ||
+ | {{Pipe}} | ||
+ | {{Pipe}}'''Volocity''' | ||
+ | {{Pipe}}'''Manual Tracking''' | ||
+ | {{Pipe}}- | ||
+ | {{Pipe}}Pros | ||
+ | {{Pipe}}Lower error in terms of tracking centroid than other tracking software. <br> Less time consuming. | ||
+ | {{Pipe}}Able to discern cells visually. <br> Able track over larger number of frames. | ||
+ | {{Pipe}}- | ||
+ | {{Pipe}}Cons | ||
+ | {{Pipe}}Failure to track cells continuously over a long number of frames > 70. <br> Biased to cells which run, rather than tumble. <br> Failure to discern motile from immotile or dead cells. | ||
+ | {{Pipe}}Time consuming. <br> Higher error in terms of tracking centroid as compared to tracking software. | ||
+ | {{Pipe}}- | ||
+ | {{Pipe}}} | ||
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- | + | ======Manual tracking will be used to track ''B. subtilis''.====== | |
|}} | |}} | ||
- | {{Imperial/EndPage}} | + | |
+ | {{Imperial/EndPage|Motility|Motility}} |