{"id":19998766,"url":"https://github.com/quantixed/volumefinder","last_synced_at":"2026-02-13T20:07:36.819Z","repository":{"id":100276194,"uuid":"51834870","full_name":"quantixed/VolumeFinder","owner":"quantixed","description":"Volume analysis of 3D point sets in IgorPro","archived":false,"fork":false,"pushed_at":"2017-03-09T11:37:37.000Z","size":2115,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-06-16T21:45:24.603Z","etag":null,"topics":["igor","microtubule","spatial-analysis","spatial-statistics","volume-analysis"],"latest_commit_sha":null,"homepage":null,"language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2016-02-16T12:41:03.000Z","updated_at":"2017-03-02T14:57:21.000Z","dependencies_parsed_at":"2023-05-13T09:45:31.160Z","dependency_job_id":null,"html_url":"https://github.com/quantixed/VolumeFinder","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/quantixed/VolumeFinder","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2FVolumeFinder","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2FVolumeFinder/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2FVolumeFinder/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2FVolumeFinder/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/quantixed","download_url":"https://codeload.github.com/quantixed/VolumeFinder/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2FVolumeFinder/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267073227,"owners_count":24031547,"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":"2025-07-25T02:00:09.625Z","response_time":70,"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":["igor","microtubule","spatial-analysis","spatial-statistics","volume-analysis"],"created_at":"2024-11-13T05:09:25.927Z","updated_at":"2025-09-21T17:32:47.478Z","avatar_url":"https://github.com/quantixed.png","language":"HTML","readme":"# VolumeFinder\nProcedures for volume analysis and spatial statistics of 3D point sets in IgorPro. A detailed walkthrough of the analysis procedure is available [here](https://github.com/quantixed/VolumeFinder/blob/master/volumefinder-analysis-3d.pdf). This README contains a brief overview.\n\nTwo types of analysis are possible\n\n1. [**Volume analysis**](#volume-analysis)\n2. [**Spatial statistics**](#spatial-statistics)\n\nMicrotubules are first segmented in Amira. Amira mesh files are converted to TIFFs and skeletons using a FIJI macro [am2skel.ijm](https://github.com/quantixed/VolumeFinder/blob/master/am2skel.ijm). This process .am files to first threshold them and produce categorised 1 px thick MT trajectories in 2D (one for each z-slice). These are called skeletons. The thresholded TIFFs are used for Volume Analysis and the skeletons are used for Spatial Statistics.\n\n###Setup\n\nPlace all procedures in `User Procedures` directory which can be found in:\n\nMac: `/Users/\u003cuser\u003e/Documents/WaveMetrics`\n\nWindows: `C:\\Users\\\u003cuser\u003e\\Documents\\WaveMetrics`\n\nLoad `VFMasterproc.ipf` into a new experiment and then one of the following options:\n\n- Volume Finder\n- Spatial Analysis\n- All analysis\n- Export to R\n\nFrom the `Macros` menu.\n\n**Caution:** Igor 7 only. Most of the code will not compile or run in Igor 6.3 and below.\n\n###Volume analysis\nThis workflow measures the density of microtubules in a stack of TIFFs. Igor will compute the volume of microtubules as a density of the volume in which they are contained. This was written for analysis of segmented data from SBF-SEM (3View). \n\nTo do this call \u003ccode\u003eVolumeFinder()\u003c/code\u003e. Now, point Igor at the directory containing the TIFFs.\nYou can scale the output to real world values using \u003ccode\u003eScaleIt(xnm,ynm,znm)\u003c/code\u003e. Using the correct voxel size. This will scale the point volumes and hull volumes to µm^3.\n\n###Spatial Statistics\n\nSkeletons are processed by Igor \u003ccode\u003eFindingVectorsFromSkeleton.ipf\u003c/code\u003e to form 2D vectors which can then be used for spatial statistical analysis. Vectors are found by a linear fit to xy coordinates.\n\nIgor will produce a report which shows three spatial statistics:\n\n* A comparison of all MT vectors with the spindle axis (defined by two xyz coords at the start of the procedure). This is colour coded (with a key) to show variance in angle from the spindle axis. Histograms summarise this information (4 histograms: 1 for each pole, 1 for all angles, 1 for all angles, abs() values).\n* Two further histograms compare MTs that are longer than 60 nm are within 80 nm of other MTs. This is independent of the spindle axis.\n* A comparison between the trajectories of MT segments with ellipsoid tangents calculated from an idealised spindle.\n\nEach cell/movie is analysed as a separate pxp. Use [SummaryPXP.ipf](https://github.com/quantixed/VolumeFinder/blob/master/SummaryPXP.ipf) to make a summary report of all your data. Compare distributions using the command `MakeComparison()`.\n\n####Extra code\n\nA little tool called `checkAxis.ipf` was developed to help visualise and correct spindle axis in 3D via gizmo. Current workflow is to: 1. run the load and analysis (using input coordinates for poles); 2. use checkaxis to refine the axis (for all datasets); 3. redo the analysis.\n\n###Analysis using R\n\nThe analysis can be reproduced in R. Simply use this [R markdown file](https://github.com/quantixed/VolumeFinder/blob/master/Mitotic_spindle_modelling.Rmd), following the instructions [here](https://github.com/quantixed/VolumeFinder/blob/master/Mitotic_spindle_modelling.html). The analysis in R requires the xyz coordinates of the start and end points of all lines generated from the skeletons. These coordinates can be output in csv format using [ExportToR.ipf](https://github.com/quantixed/VolumeFinder/blob/master/ExportToR.ipf), see the instructions for further details. Alternatively, you may use some other non-Igor workflow to get the coordinates and run the analysis in R.\n\n###Calculation of SNR\n\nAn [ImageJ macro](https://github.com/quantixed/VolumeFinder/blob/master/SNR3View.ijm) will extract the mean pixel density in segmented MT regions (per slice) and calculate the SD of a halo around the MTs (excluding MTs themselves), SNR is calculated and output as a csv. [Igor code](https://github.com/quantixed/VolumeFinder/blob/master/SNR3View.ipf) Igor code is available to crunch the output.","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantixed%2Fvolumefinder","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fquantixed%2Fvolumefinder","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantixed%2Fvolumefinder/lists"}