{"id":19998832,"url":"https://github.com/quantixed/p063p036","last_synced_at":"2025-08-19T02:39:53.672Z","repository":{"id":163841100,"uuid":"614310025","full_name":"quantixed/p063p036","owner":"quantixed","description":"Data and code for manuscript p063p036","archived":false,"fork":false,"pushed_at":"2023-10-21T06:55:15.000Z","size":64613,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-01T23:28:41.224Z","etag":null,"topics":["paper"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/quantixed.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2023-03-15T10:30:05.000Z","updated_at":"2024-05-09T12:36:23.000Z","dependencies_parsed_at":null,"dependency_job_id":"eee2ba72-42a5-4861-92e7-f2add1d98092","html_url":"https://github.com/quantixed/p063p036","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/quantixed/p063p036","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2Fp063p036","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2Fp063p036/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2Fp063p036/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2Fp063p036/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/quantixed","download_url":"https://codeload.github.com/quantixed/p063p036/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2Fp063p036/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267790821,"owners_count":24144892,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-07-29T02:00:12.549Z","response_time":2574,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["paper"],"created_at":"2024-11-13T05:09:36.106Z","updated_at":"2025-07-30T01:09:16.426Z","avatar_url":"https://github.com/quantixed.png","language":"R","readme":"# p063p036\n\nCode and data for Sittewelle \u0026 Royle manuscript `#p063p036`\n\n**Passive diffusion accounts for the majority of intracellular nanovesicle transport**\n\nMéghane Sittewelle \u0026 Stephen J. Royle\n\n*Life Sci Alliance* 2023. DOI: [hhttps://doi.org/10.26508/lsa.202302406](https://doi.org/10.26508/lsa.202302406)\n\n## plots\n\nR code for plot recreation.\nFor details, see the README in `plots/`\n\n- Several R scripts require **TrackMateR** to run.\nStable release is [here](https://doi.org/10.5281/zenodo.7042948), development version is [here](https://github.com/quantixed/TrackMateR).\n- Some R scripts require TrackMate XML files to process data and generate plots.\nThese files are available at [Zenodo](https://doi.org/10.5281/zenodo.7905013) together with some of the visualizations generated using TrackMateR.\n\n\n## simulations\n\n### Modelling particle diffusion\n\nFor FLIP simulation, `DiffusionSim.ipf` is written for IGOR Pro.\n\n\u003cdetails\u003e\n\t\u003csummary\u003eA GUI is available to guide simulations. Click for details...\u003c/summary\u003e\n\t\n\u003cimg src=\"img/VesiclePanel.png\" width=\"300\"\u003e\n\n- Most variables are self-explanatory, please note the units.\n- *FLIP mode* selects between a circle (used in the paper), square or a ring.\n- *Random start location* when checked will start vesicles at random locations throughout the cell. When unchecked, vesicles will start at the cell centre.\n- Specify bleach location for circle, square and ring. FlipRingR stipulates the radius of the ring (intended to be used without Random start location checked) so that vesicles diffuse away from the origin before entering the ring. For square specify the left-top (LT) and right-bottom (RB) XY locations relative to the cell centre `(0,0)`. For circle, an offset can be specified as well as a radius.\n- *Simulate* will show the movement of vesicles without FLIP\n- *FLIP* will do a single FLIP simulation\n- *FLIP Rep* will do repeated FLIP simulations\n- *Visualise* if checked will show the tracks when FLIP Rep is clicked.\n\nThe bottom part of the panel allows the simulations to be automated by taking a variable number of steps from a start and stop point for FLIP circle radius and for the diffusion coefficient (as described in the paper. Click *Automate* to start after setting all parameters.\n\n\n\u003c/details\u003e\n\n### Simulating particle diffusion and benchmarking TrackMate\n\nParticle movies were generated using `Particle_Simulation.ijm` in FIJI.\nTrackMate automation is via the groovy script `TrackMateAutomation.groovy`.\nThe ground truth outputs can be evaluated in IGOR using `VesicleTracks.ipf`.\nSelect *Macros \u003e Vesicle Tracks Only* or *Macros \u003e Vesicle Tracks Simple* and select the csv file of the ground truth data that you would like to evaluate.\nThe \"simple\" workflow skips algorithmic comparison of tracks and other features which are not necessary for evaluating the ground truth data.\n\n\u003cdetails\u003e\n\t\u003csummary\u003eAlthough not documented in the paper, `VesicleTracks.ipf` will also display movies and tracking data in a neat widget for visualization. Click for details...\u003c/summary\u003e\n\t\n\u003cimg src=\"img/VesicleTracks.png\" width=\"400\"\u003e\n\nTo use this, select *Macros \u003e Vesicle Tracks...* As an input it requires a csv file of tracks and an image.\nThis is compatible with the outputs from `Particle_Simulation.ijm` but the display will show all particles in the volume.\n\n\u003cimg src=\"img/VesicleTracks.gif\" width=\"302\"\u003e\n\nThe default view shows all particles. Click \"show selected\" to see the top most directed tracks according to the program. \n\n\u003c/details\u003e\n\nThe TrackMate XML outputs can be analyzed using `TrackMateR`.\nR code to evaluate TrackMate XML files from these routines is available in `plots/SJR194/`.\n\nSome IGOR procedure files require `PXPUtils.ipf` to run properly, available [here](https://github.com/quantixed/PXPUtils).","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantixed%2Fp063p036","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fquantixed%2Fp063p036","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantixed%2Fp063p036/lists"}