| _version_ | 1866901938930450432 |
|---|---|
| author | Higgins, Daniel |
| author_facet | Higgins, Daniel |
| contents | <p><strong>1. Scripts for rotating confocal images (RotatorR01) in imageJ.</strong><br><br><strong>2. Adaptation of mitoMAPR</strong> (Yue Zhang, Anne Lanjuin, Suvagata Roy Chowdhury, Meeta Mistry, Carlos G Silva-García, Heather J Weir, Chia-Lin Lee, Caroline C Escoubas, Emina Tabakovic, William B Mair (2019) Neuronal TORC1 modulates longevity via AMPK and cell nonautonomous regulation of mitochondrial dynamics in C. elegans eLife 8:e49158). We adapted the code to allow batch processing and to configure parameters prior to running.<br><br><strong>3. Puntca process</strong> </p> <p>The Puncta Process ImageJ PlugIn is a <a href="https://en.wikipedia.org/wiki/Particle_Analysis">practical analysis</a> tool for counting puncta in 3D image data.</p> <p>The plugin uses single-channel data to produce three specific values:</p> <ul> <li><strong>Puncta Volume</strong> An average number of voxels (volume picture elements) of the object times z,y, and z calibrations.</li> <li><strong>Puncta Number</strong> The average number of puncta counts within a given ROI (Region of Interest)</li> <li><strong>ROI Intensity</strong> The measures the overall pixel intensity over the Region of Interest</li> </ul> <p>The Puncta Process expects that the preprocessing step of selecting the ROIs has been completed and that the image data is separated into a directory structure based on fluorescence (488, 561)</p> <p>The Puncta Process leverages the <a href="https://imagej.github.io/plugins/morpholibj">MorphoLibJ</a> and <a href="https://imagej.github.io/plugins/3d-objects-counter">3D Objects Counter</a> PlugIns and allows users to select Filter options and threshold levels prior to process execution.</p> <p>The process provides detailed outputs of each process step, including:</p> <ul> <li>White Top Hat corrected images</li> <li>3D Object Counter details (CSV)</li> <li>Z Projected images (maximum intensity)</li> </ul> <p>And a summary output including:</p> <ul> <li>MS Excel Report</li> <li>Preliminary Visualizations BarCharts with Error bar</li> <li>Summary CSV data (for ease of import into downstream processes)</li> </ul> <h2>Installation</h2> <ul> <li>In <a href="https://imagej.net/software/fiji">Fiji</a>), you just need to <a href="https://imagej.net/update-sites/following#add-update-sites">add</a> the Puncta Process and IJPB-plugins sites to your list of update sites: <ol> <li>Select Help › Update… from the menu to start the <a href="https://imagej.net/plugins/updater">updater</a>.</li> <li>Click on <em>Manage update sites</em>. This brings up a dialog where you can activate additional update sites.</li> <li>Activate the <strong>Puncta Process</strong> and <strong>IJPB-plugins</strong> sites and close the dialog.</li> <li>Click <em>Apply changes</em> and restart ImageJ.</li> </ol> </li> </ul> <h2>Resources</h2> <p>The main source code directory is on GitHub under <a href="https://github.com/DanHUMassMed/puncta_process_plugin">here</a>.</p> <p><br><br></p> <p> </p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_17495841 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | ImageJ scripts for counting puncta and mitochondrial networks. Higgins, Daniel <p><strong>1. Scripts for rotating confocal images (RotatorR01) in imageJ.</strong><br><br><strong>2. Adaptation of mitoMAPR</strong> (Yue Zhang, Anne Lanjuin, Suvagata Roy Chowdhury, Meeta Mistry, Carlos G Silva-García, Heather J Weir, Chia-Lin Lee, Caroline C Escoubas, Emina Tabakovic, William B Mair (2019) Neuronal TORC1 modulates longevity via AMPK and cell nonautonomous regulation of mitochondrial dynamics in C. elegans eLife 8:e49158). We adapted the code to allow batch processing and to configure parameters prior to running.<br><br><strong>3. Puntca process</strong> </p> <p>The Puncta Process ImageJ PlugIn is a <a href="https://en.wikipedia.org/wiki/Particle_Analysis">practical analysis</a> tool for counting puncta in 3D image data.</p> <p>The plugin uses single-channel data to produce three specific values:</p> <ul> <li><strong>Puncta Volume</strong> An average number of voxels (volume picture elements) of the object times z,y, and z calibrations.</li> <li><strong>Puncta Number</strong> The average number of puncta counts within a given ROI (Region of Interest)</li> <li><strong>ROI Intensity</strong> The measures the overall pixel intensity over the Region of Interest</li> </ul> <p>The Puncta Process expects that the preprocessing step of selecting the ROIs has been completed and that the image data is separated into a directory structure based on fluorescence (488, 561)</p> <p>The Puncta Process leverages the <a href="https://imagej.github.io/plugins/morpholibj">MorphoLibJ</a> and <a href="https://imagej.github.io/plugins/3d-objects-counter">3D Objects Counter</a> PlugIns and allows users to select Filter options and threshold levels prior to process execution.</p> <p>The process provides detailed outputs of each process step, including:</p> <ul> <li>White Top Hat corrected images</li> <li>3D Object Counter details (CSV)</li> <li>Z Projected images (maximum intensity)</li> </ul> <p>And a summary output including:</p> <ul> <li>MS Excel Report</li> <li>Preliminary Visualizations BarCharts with Error bar</li> <li>Summary CSV data (for ease of import into downstream processes)</li> </ul> <h2>Installation</h2> <ul> <li>In <a href="https://imagej.net/software/fiji">Fiji</a>), you just need to <a href="https://imagej.net/update-sites/following#add-update-sites">add</a> the Puncta Process and IJPB-plugins sites to your list of update sites: <ol> <li>Select Help › Update… from the menu to start the <a href="https://imagej.net/plugins/updater">updater</a>.</li> <li>Click on <em>Manage update sites</em>. This brings up a dialog where you can activate additional update sites.</li> <li>Activate the <strong>Puncta Process</strong> and <strong>IJPB-plugins</strong> sites and close the dialog.</li> <li>Click <em>Apply changes</em> and restart ImageJ.</li> </ol> </li> </ul> <h2>Resources</h2> <p>The main source code directory is on GitHub under <a href="https://github.com/DanHUMassMed/puncta_process_plugin">here</a>.</p> <p><br><br></p> <p> </p> |
| title | ImageJ scripts for counting puncta and mitochondrial networks. |
| url | https://doi.org/10.5281/zenodo.17495841 |