Show pageOld revisionsBacklinksBack to top This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong. ~~NOTOC~~ <WRAP twothirds column leftalign> ====== 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-friendly GUI, designed to minimise the number of parameters that must be chosen and maximise immediate user feedback for those that do. * Flexible design, accommodating a range of different workflows and dataset types. * Rapid algorithms with low memory requirements, allowing thousands of objects to be tracked simultaneously on a standard laptop computer. * Integrated overlay and plotting systems, allowing rapid validation and visualisation of tracking data. * No need for a Matlab license - FAST is also available as a free stand-alone application. Sound good? Download the latest distribution of the Matlab files [[https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/FASTdownloads/FAST_v2_1.zip|here]], the stand-alone version [[setup:Installers|here]], or see the [[setup:installation|installation guide]] for more details on how to perform the download and setup process. </WRAP> <WRAP third column centeralign> {{ :textlogolarge.png?nolink&400 }} <WRAP group> <WRAP quarter column centeralign> [[https://mackdurham.group.shef.ac.uk/FAST_DokuWiki/FASTdownloads/FAST_v2_1.zip|{{ :logos:downloadbutton.png?75 }}]] Download </WRAP> <WRAP quarter column centeralign> [[https://github.com/Pseudomoaner/FAST|{{ :logos:githublogo.png?75 }}]] Code </WRAP> <WRAP quarter column centeralign> [[https://figshare.com/projects/FAST_demonstration_data/155852|{{ :logos:figshare.png?75 }}]] Examples </WRAP> <WRAP quarter column centeralign> [[https://doi.org/10.1371/journal.pcbi.1011524|{{ :plos-one-vector-logo.png?75 }}]] Paper </WRAP> </WRAP> </WRAP> ===== Introduction to FAST ===== {{ youtube>9rDLSZ2AcQ0?large }} ===== The FAST modules ===== <WRAP group> <WRAP third column centeralign> === Segmentation === [[usage:segmentation|{{ :logos:segmentation.png?nolink&200 }}]] The segmentation module allows you to automatically isolate individual objects from your images. </WRAP> <WRAP third column centeralign> === Feature detection === [[usage:feature_extraction|{{ :logos:features.png?nolink&200 }}]] Feature detection quantifies properties of the objects detected by the segmentation module. </WRAP> <WRAP third column centeralign> === Tracking === [[usage:tracking|{{ :logos:tracking.png?nolink&200 }}]] Tracking links together objects between timepoints. A [[usage:track_correction|sub-GUI]] also allows manual correction of tracks. </WRAP> </WRAP> <WRAP group> <WRAP third column centeralign> === Division detection === [[usage:division_detection|{{ :logos:divisions.png?nolink&200 }}]] Many biological samples consist of cells that repeatedly divide. This module allows you to detect such divisions and reconstruct lineages. </WRAP> <WRAP third column centeralign> === Overlays === [[usage:overlays|{{ :logos:overlays.png?nolink&200 }}]] Overlaying extracted data on top of raw images can provide powerful visualisations of your system. </WRAP> <WRAP third column centeralign> === Plotting === {{ :logos:plotting.png?nolink&200 ||usage:plotting}} The plotting module allows you to quickly assess relationships between features and variables extracted during tracking. </WRAP> </WRAP> ==== Funding and support ==== We are grateful for funding from the EPSRC and BBSRC, grant codes EP/F500394/1 and BB/R018383/1. <WRAP group> <WRAP quarter column centeralign> {{ ::ukri_bbsrc.png?nolink&300 |https://bbsrc.ukri.org/}} </WRAP> <WRAP quarter column centeralign> {{ ::ukri_epsrc.png?nolink&300 |https://epsrc.ukri.org/}} </WRAP> <WRAP quarter column centeralign> {{ ::tuos_primary_logo_full_colour.png?nolink&230 |https://www.sheffield.ac.uk/physics/}} </WRAP> <WRAP quarter column centeralign> {{ ::university-of-oxford.png?nolink&300 |http://www.dtc.ox.ac.uk/}} </WRAP> </WRAP> start.txt Last modified: 2023/10/10 11:19by pseudomoaner