FAST
https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/dokuwiki/
2024-03-29T08:24:15+00:00FAST
https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/dokuwiki/
https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/dokuwiki/lib/exe/fetch.php?media=favicon.icotext/html2023-10-10T11:19:54+00:00pseudomoaner (pseudomoaner@undisclosed.example.com)start
https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/dokuwiki/doku.php?id=start&rev=1696933194&do=diff
FAST, the Feature-Assisted Segmenter/Tracker
Have you struggled with automated measurement of the movement of many closely-packed individuals? The Durham lab's tracking system, FAST, may be the answer to your problems. Its features include:
* A user-friendlytext/html2023-10-10T11:19:07+00:00pseudomoaner (pseudomoaner@undisclosed.example.com)plos-one-vector-logo.png - created
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https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/dokuwiki/doku.php?id=extra:contact_information&rev=1696932971&do=diff
Contact information
How to cite FAST
If you find FAST useful, please include the following citation in any publications you produce using it:
* Meacock, O. J, Durham, W. M, Tracking bacteria at high density with FAST, the Feature-Assisted Segmenter/Trackertext/html2023-07-05T15:36:33+00:00pseudomoaner (pseudomoaner@undisclosed.example.com)usage:division_detection - [The Division Detection module]
https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/dokuwiki/doku.php?id=usage:division_detection&rev=1688567793&do=diff
The Division Detection module
In the tracking module, we sought the optimal way to integrate feature information to pair detected objects between frames. Division detection is conceptually similar, but instead of linking one object to another we wish to optimally use feature information to pair each mother cell with two daughter cells. This is achieved using a similar algorithm to the tracking module, with a few key modifications:$R$$R$text/html2023-07-05T15:36:09+00:00pseudomoaner (pseudomoaner@undisclosed.example.com)usage:divisiondetectionv2.png - created
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https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/dokuwiki/doku.php?id=post:labelunusualevents.m&rev=1678227811&do=diff
labelUnusualEvents.m
Class: Function
Description: Takes in the procTracks data structure and detects events based on the times at which the values of a user-specified field move a specified distance either above or below the track-level average. The specified distance is based on the population-level estimate of the variance of the variable, multiplied by a user-selected factor.text/html2023-03-07T22:18:53+00:00pseudomoaner (pseudomoaner@undisclosed.example.com)post:post-processing_toolbox - [Event labelling]
https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/dokuwiki/doku.php?id=post:post-processing_toolbox&rev=1678227533&do=diff
Post-processing toolbox
Once you have performed object tracking, there are many tasks that you may wish to perform with that tracking data. This page lists a number of scripts that can be downloaded that perform various post-processing tasks on FAST's track output.text/html2022-11-15T11:25:28+00:00pseudomoaner (pseudomoaner@undisclosed.example.com)setup:installers
https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/dokuwiki/doku.php?id=setup:installers&rev=1668511528&do=diff
Installers
On this page, you can find the platform-specific installers for the current stand-alone version of FAST (v2.0.1). Please select one of the options below:
Windows
<https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/FASTdownloads/FAST_v2_1_Installer_Win.exe>
Linux
<https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/FASTdownloads/FAST_v2_1_Installer_Lnx.install>
Compiled in Ubuntu v20.04
macOS
<https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/FASTdownloads/FAST_v2_1_Installer_Mac.a…text/html2022-11-15T11:24:34+00:00pseudomoaner (pseudomoaner@undisclosed.example.com)setup:installation
https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/dokuwiki/doku.php?id=setup:installation&rev=1668511474&do=diff
Installation
As FAST has been developed in Matlab, you can download its unencrypted .m and .fig files and run it directly from Matlab's command line. This option allows you to make direct modifications to FAST's code, necessary for some advanced capabilities. It also allows use of FAST'stext/html2022-10-20T10:35:29+00:00pseudomoaner (pseudomoaner@undisclosed.example.com)usage:segmentation
https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/dokuwiki/doku.php?id=usage:segmentation&rev=1666258529&do=diff
The Segmentation module
In the first stage of the FAST pipeline, individual objects are segmented from the background. FAST's segmentation routine is integral to its ability to track objects in high-density systems, as it permits automated separation of thousands of closely-packed objects.text/html2022-09-05T23:05:50+00:00pseudomoaner (pseudomoaner@undisclosed.example.com)extra:publications_using_fast
https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/dokuwiki/doku.php?id=extra:publications_using_fast&rev=1662415550&do=diff
Publications using FAST
* Granato, E. T, Foster, K. R, The evolution of mass cell suicide in bacterial warfare, Curr. Bio. (2020) 30 pp 1-8, doi: <https://doi.org/10.1016/j.cub.2020.05.007>
* Meacock, O. J, Doostmohammadi, A, Foster, K. R, Yeomans, J. M, Durham, W. M, Bacteria solve the problem of crowding by moving slowlytext/html2022-09-05T23:05:29+00:00pseudomoaner (pseudomoaner@undisclosed.example.com)usage:advanced_usage
https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/dokuwiki/doku.php?id=usage:advanced_usage&rev=1662415529&do=diff
Advanced usage
As well as the general workflow described in the previous pages, FAST can be flexibly adapted to support more specific analytical tasks.
Non-standard workflows
Although FAST contains all the essential tools for a complete image to track workflow, some users may wish to extend and adjust portions of this workflow. For example, you may find that a different segmentation algorithm is more effective at analysing your data than FAST's inbuilt segmentation module, or that you need t…text/html2022-09-05T23:05:15+00:00pseudomoaner (pseudomoaner@undisclosed.example.com)usage:plotting
https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/dokuwiki/doku.php?id=usage:plotting&rev=1662415515&do=diff
The Plotting module
With the plotting module, you can explore your track data through a simple, user-friendly interface. As well as those tools available by default, the plotting module also supports certain types of user-defined data, described in thetext/html2022-09-05T23:04:56+00:00pseudomoaner (pseudomoaner@undisclosed.example.com)usage:overlays
https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/dokuwiki/doku.php?id=usage:overlays&rev=1662415496&do=diff
The Overlays module
The overlays module allows you to visualise the output of tracking and post-processing in the context of the raw images that form your dataset. This allows you to visually verify the accuracy of your data processing, and can also provide novel insights into spatial and temporal structure in your dataset.text/html2022-07-18T23:32:38+00:00pseudomoaner (pseudomoaner@undisclosed.example.com)post:coarsegraindemo.jpg - created
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