<?xml version="1.0" encoding="utf-8"?>
<export-example>
  <doc>
    <id>10132</id>
    <completedYear/>
    <publishedYear>2025</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Semi-automatic Geometrical Reconstruction and Analysis of Filopodia Dynamics in 4D Two-Photon Microscopy Images</title>
    <abstract language="eng">Background: &#13;
Filopodia are thin and dynamic membrane protrusions that play a crucial role in cell migration, axon guidance, and other processes where cells explore and interact with their surroundings. Historically, filopodial dynamics have been studied in great detail in 2D in cultured cells, and more recently in 3D culture as well as living brains. However, there is a lack of efficient tools to trace and track filopodia in 4D images of complex brain cells. &#13;
&#13;
Results: &#13;
To address this issue, we have developed a semi-automatic workflow for tracing filopodia in 3D images and tracking the traced filopodia over time. The workflow was developed based on high-resolution data of photoreceptor axon terminals in the in vivo context of normal Drosophila brain development, but devised to be applicable to filopodia in any system, including at different temporal and spatial scales. In contrast to the pre-existing methods, our workflow relies solely on the original intensity images without the requirement for segmentation or complex preprocessing. The workflow was realized in C++ within the Amira software system and consists of two main parts, dataset pre-processing, and geometrical filopodia reconstruction, where each of the two parts comprises multiple steps. In this paper, we provide an extensive workflow description and demonstrate its versatility for two different axo-dendritic morphologies, R7 and Dm8 cells. Finally, we provide an analysis of the time requirements for user input and data processing.&#13;
&#13;
Conclusion: &#13;
To facilitate simple application within Amira or other frameworks, we share the source code, which is available athttps://github.com/zibamira/filopodia-tool.</abstract>
    <parentTitle language="deu">bioRxiv</parentTitle>
    <identifier type="doi">10.1101/2025.05.20.654789</identifier>
    <enrichment key="opus_doi_flag">true</enrichment>
    <enrichment key="opus_doi_json">{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2025,5,24]],"date-time":"2025-05-24T15:10:09Z","timestamp":1748099409112,"version":"3.41.0"},"posted":{"date-parts":[[2025,5,21]]},"group-title":"Neuroscience","reference-count":33,"publisher":"Cold Spring Harbor Laboratory","license":[{"start":{"date-parts":[[2025,5,21]],"date-time":"2025-05-21T00:00:00Z","timestamp":1747785600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"crossref","award":["Research Unit 5289 RobustCircuit, project Z","CRC 958"],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]},{"award":["Grant agreement no. 101019191"],"id":[{"id":"https:\/\/ror.org\/0472cxd90","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,5,22]]},"abstract":"&lt;jats:title&gt;Abstract&lt;\/jats:title&gt;&lt;jats:sec&gt;&lt;jats:title&gt;Background&lt;\/jats:title&gt;&lt;jats:p&gt;Filopodia are thin and dynamic membrane protrusions that play a crucial role in cell migration, axon guidance, and other processes where cells explore and interact with their surroundings. Historically, filopodial dynamics have been studied in great detail in 2D in cultured cells, and more recently in 3D culture as well as living brains. However, there is a lack of efficient tools to trace and track filopodia in 4D images of complex brain cells.&lt;\/jats:p&gt;&lt;\/jats:sec&gt;&lt;jats:sec&gt;&lt;jats:title&gt;Results&lt;\/jats:title&gt;&lt;jats:p&gt;To address this issue, we have developed a semi-automatic workflow for tracing filopodia in 3D images and tracking the traced filopodia over time. The workflow was developed based on high-resolution data of photoreceptor axon terminals in the in vivo context of normal&lt;jats:italic&gt;Drosophila&lt;\/jats:italic&gt;brain development, but devised to be applicable to filopodia in any system, including at different temporal and spatial scales. In contrast to the pre-existing methods, our workflow relies solely on the original intensity images without the requirement for segmentation or complex preprocessing. The workflow was realized in C++ within the&lt;jats:italic&gt;Amira&lt;\/jats:italic&gt;software system and consists of two main parts, dataset pre-processing, and geometrical filopodia reconstruction, where each of the two parts comprises multiple steps. In this paper, we provide an extensive workflow description and demonstrate its versatility for two different axo-dendritic morphologies, R7 and Dm8 cells. Finally, we provide an analysis of the time requirements for user input and data processing.&lt;\/jats:p&gt;&lt;\/jats:sec&gt;&lt;jats:sec&gt;&lt;jats:title&gt;Conclusion&lt;\/jats:title&gt;&lt;jats:p&gt;To facilitate simple application within&lt;jats:italic&gt;Amira&lt;\/jats:italic&gt;or other frameworks, we share the source code, which is available at&lt;jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/zibamira\/filopodia-tool\"&gt;https:\/\/github.com\/zibamira\/filopodia-tool&lt;\/jats:ext-link&gt;.&lt;\/jats:p&gt;&lt;\/jats:sec&gt;","DOI":"10.1101\/2025.05.20.654789","type":"posted-content","created":{"date-parts":[[2025,5,21]],"date-time":"2025-05-21T22:10:16Z","timestamp":1747865416000},"source":"Crossref","is-referenced-by-count":0,"title":["Semi-automatic Geometrical Reconstruction and Analysis of Filopodia Dynamics in 4D Two-Photon Microscopy Images"],"prefix":"10.1101","author":[{"given":"Bla\u017e","family":"Brence","sequence":"first","affiliation":[]},{"given":"Josephine","family":"Brummer","sequence":"additional","affiliation":[]},{"given":"Vincent J.","family":"Dercksen","sequence":"additional","affiliation":[]},{"given":"Mehmet Neset","family":"\u00d6zel","sequence":"additional","affiliation":[]},{"given":"Abhishkek","family":"Kulkarni","sequence":"additional","affiliation":[]},{"given":"Neele","family":"Wolterhoff","sequence":"additional","affiliation":[]},{"given":"Steffen","family":"Prohaska","sequence":"additional","affiliation":[]},{"given":"Peter Robin","family":"Hiesinger","sequence":"additional","affiliation":[]},{"given":"Daniel","family":"Baum","sequence":"additional","affiliation":[]}],"member":"246","reference":[{"key":"2025052407501029000_2025.05.20.654789v2.1","doi-asserted-by":"publisher","DOI":"10.1016\/j.semcdb.2022.03.038"},{"key":"2025052407501029000_2025.05.20.654789v2.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ydbio.2018.08.015"},{"key":"2025052407501029000_2025.05.20.654789v2.3","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-cellbio-020223-025210"},{"key":"2025052407501029000_2025.05.20.654789v2.4","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.10721"},{"key":"2025052407501029000_2025.05.20.654789v2.5","doi-asserted-by":"publisher","DOI":"10.1126\/science.adk3043"},{"key":"2025052407501029000_2025.05.20.654789v2.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2020.107907"},{"key":"2025052407501029000_2025.05.20.654789v2.7","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2114856118"},{"key":"2025052407501029000_2025.05.20.654789v2.8","doi-asserted-by":"publisher","DOI":"10.1038\/s41593-022-01086-6"},{"key":"2025052407501029000_2025.05.20.654789v2.9","doi-asserted-by":"publisher","DOI":"10.1101\/506378"},{"key":"2025052407501029000_2025.05.20.654789v2.10","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-14781-4"},{"key":"2025052407501029000_2025.05.20.654789v2.11","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2021.110145"},{"key":"2025052407501029000_2025.05.20.654789v2.12","doi-asserted-by":"publisher","DOI":"10.1016\/s1361-8415(02)00110-x"},{"key":"2025052407501029000_2025.05.20.654789v2.13","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.201306067"},{"key":"2025052407501029000_2025.05.20.654789v2.14","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.201501081"},{"key":"2025052407501029000_2025.05.20.654789v2.15","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.201705113"},{"key":"2025052407501029000_2025.05.20.654789v2.16","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-7-66"},{"key":"2025052407501029000_2025.05.20.654789v2.17","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.201704045"},{"key":"2025052407501029000_2025.05.20.654789v2.18","doi-asserted-by":"publisher","DOI":"10.1091\/mbc.E16-06-0406"},{"key":"2025052407501029000_2025.05.20.654789v2.19","doi-asserted-by":"publisher","DOI":"10.1016\/j.jneumeth.2014.08.016"},{"key":"2025052407501029000_2025.05.20.654789v2.20","doi-asserted-by":"publisher","DOI":"10.1002\/dneu.20866"},{"key":"2025052407501029000_2025.05.20.654789v2.21","doi-asserted-by":"publisher","DOI":"10.1016\/j.jneumeth.2008.02.009"},{"key":"2025052407501029000_2025.05.20.654789v2.22","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-11443-y"},{"key":"2025052407501029000_2025.05.20.654789v2.23","doi-asserted-by":"publisher","DOI":"10.1109\/TMI.2018.2873842"},{"key":"2025052407501029000_2025.05.20.654789v2.24","doi-asserted-by":"publisher","DOI":"10.1101\/2020.12.10.420414"},{"key":"2025052407501029000_2025.05.20.654789v2.25","doi-asserted-by":"publisher","DOI":"10.1109\/ISBI56570.2024.10635109"},{"key":"2025052407501029000_2025.05.20.654789v2.26","doi-asserted-by":"publisher","DOI":"10.1016\/B978-012387582-2\/50040-X"},{"key":"2025052407501029000_2025.05.20.654789v2.27","doi-asserted-by":"publisher","DOI":"10.1007\/s12021-013-9213-2"},{"key":"2025052407501029000_2025.05.20.654789v2.28","doi-asserted-by":"publisher","DOI":"10.1002\/9780470744055"},{"key":"2025052407501029000_2025.05.20.654789v2.29","unstructured":"Johnson, H.J. , McCormick, M.M. , Ib\u00e1\u00f1ez, L. , Consortium, I.S. : The ITK Software Guide: Introduction and Development Guidelines. The ITK Software Guide: ITK 4.7. Kitware, ??? (2015)"},{"key":"2025052407501029000_2025.05.20.654789v2.30","doi-asserted-by":"publisher","DOI":"10.1016\/S0925-7721(02)00093-7"},{"key":"2025052407501029000_2025.05.20.654789v2.31","doi-asserted-by":"publisher","DOI":"10.1007\/BF01386390"},{"key":"2025052407501029000_2025.05.20.654789v2.32","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3713"},{"key":"2025052407501029000_2025.05.20.654789v2.33","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2023.12.037"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.05.20.654789","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,24]],"date-time":"2025-05-24T14:50:17Z","timestamp":1748098217000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.05.20.654789"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,21]]},"references-count":33,"URL":"https:\/\/doi.org\/10.1101\/2025.05.20.654789","relation":{},"subject":[],"published":{"date-parts":[[2025,5,21]]},"subtype":"preprint"}}</enrichment>
    <enrichment key="opus_crossrefLicence">http://creativecommons.org/licenses/by-nc/4.0/</enrichment>
    <enrichment key="opus_import_origin">crossref</enrichment>
    <enrichment key="opus_doiImportPopulated">PersonAuthorFirstName_1,PersonAuthorLastName_1,PersonAuthorFirstName_2,PersonAuthorLastName_2,PersonAuthorFirstName_3,PersonAuthorLastName_3,PersonAuthorFirstName_4,PersonAuthorLastName_4,PersonAuthorFirstName_5,PersonAuthorLastName_5,PersonAuthorFirstName_6,PersonAuthorLastName_6,PersonAuthorFirstName_7,PersonAuthorLastName_7,PersonAuthorFirstName_8,PersonAuthorLastName_8,PersonAuthorFirstName_9,PersonAuthorLastName_9,PublisherName,TitleMain_1,TitleAbstract_1,PublishedYear,Enrichmentopus_crossrefLicence</enrichment>
    <enrichment key="SubmissionStatus">accepted for publication</enrichment>
    <enrichment key="opus.source">doi-import</enrichment>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Blaž Brence</author>
    <submitter>Blaž Brence</submitter>
    <author>Josephine Brummer</author>
    <author>Vincent J. Dercksen</author>
    <author>Mehmet Neset Özel</author>
    <author>Abhishkek Kulkarni</author>
    <author>Neele Wolterhoff</author>
    <author>Steffen Prohaska</author>
    <author>Peter Robin Hiesinger</author>
    <author>Daniel Baum</author>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <collection role="persons" number="brence">Brence, Blaž</collection>
    <collection role="projects" number="ROBUSTCIRCUIT">ROBUSTCIRCUIT</collection>
  </doc>
</export-example>
