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Export Date: 12 July 2022
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Correspondence Address: Horváth, P.; Synthetic and Systems Biology Unit, Hungary; email: horvath.peter@brc.hu
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AnnotatorJ combines single-cell identification with deep learning (DL) and manual annotation. Cellular analysis quality depends on accurate and reliable detection and segmentation of cells so that the subsequent steps of analyses, for example, expression measurements, may be carried out precisely and without bias. DL has recently become a popular way of segmenting cells, performing unimaginably better than conventional methods. However, such DL applications may be trained on a large amount of annotated data to be able to match the highest expectations. High-quality annotations are unfortunately expensive as they require field experts to create them, and often cannot be shared outside the lab due to medical regulations. We propose AnnotatorJ, an ImageJ plugin for the semiautomatic annotation of cells (or generally, objects of interest) on (not only) microscopy images in 2D that helps find the true contour of individual objects by applying U-Net-based presegmentation. The manual labor of hand annotating cells can be significantly accelerated by using our tool. Thus, it enables users to create such datasets that could potentially increase the accuracy of state-of-the-art solutions, DL or otherwise, when used as training data.
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<div class="JournalArticle Publication short-list"> <div class="authors"> <span class="author-name" mtid="10071425"> <a href="/gui2/?type=authors&mode=browse&sel=10071425" target="_blank">Hollandi, Reka</a> </span> <span class="author-type"> </span> ; <span class="author-name" mtid="10071366"> <a href="/gui2/?type=authors&mode=browse&sel=10071366" target="_blank">Diosdi, Akos</a> </span> <span class="author-type"> </span> ; <span class="author-name" mtid="10074578"> <a href="/gui2/?type=authors&mode=browse&sel=10074578" target="_blank">Hollandi, Gabor</a> </span> <span class="author-type"> </span> ; <span class="author-name" mtid="10074070"> <a href="/gui2/?type=authors&mode=browse&sel=10074070" target="_blank">Moshkov, Nikita</a> </span> <span class="author-type"> </span> ; <span class="author-name" mtid="10030964"> <a href="/gui2/?type=authors&mode=browse&sel=10030964" target="_blank">Horvath, Peter ✉</a> </span> <span class="author-type"> </span> </div ><div class="title"><a href="/gui2/?mode=browse¶ms=publication;31612924" mtid="31612924" target="_blank">AnnotatorJ: an ImageJ plugin to ease hand annotation of cellular compartments</a></div> <div class="pub-info"> <span class="journal-title">MOLECULAR BIOLOGY OF THE CELL</span> <span class="journal-volume">31</span> : <span class="journal-issue">20</span> <span class="page"> pp. 2179-2186. , 8 p. </span> <span class="year">(2020)</span> </div> <div class="pub-end"><div class="identifier-list"> <span class="identifiers"> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="10.1091/mbc.E20-02-0156" target="_blank" href="https://doi.org/10.1091/mbc.E20-02-0156"> DOI </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="000569165000005" target="_blank" href="https://www.webofscience.com/wos/woscc/full-record/000569165000005"> WoS </a> </span> <span class="id identifier oa_GREEN" title=" Green "> <a style="color:black" title="117709" target="_blank" href="http://real.mtak.hu/117709"> REAL </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="85091126240" target="_blank" href="http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-85091126240"> Scopus </a> </span> <span class="id identifier oa_none" title="none"> <a style="color:blue" title="32697683" target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=32697683&dopt=Abstract"> PubMed </a> </span> </span> </div> <div class="short-pub-prop-list"> <span class="deleted-record">Zárolt</span> <span class="short-pub-mtid"> Közlemény:31612924 </span> <span class="status-holder"><span class="status-data status-VALIDATED"> Egyeztetett </span></span> <span class="pub-core">Forrás Idéző </span> <span class="pub-type">Folyóiratcikk (Rövid közlemény ) </span> <!-- && !record.category.scientific --> <span class="pub-category">Tudományos</span> <div class="publication-citation" style="margin-left: 0.5cm;"> <span title="Nyilvános idézőközlemények összesen, említések nélkül" class="citingPub-count">Nyilvános idéző összesen: 19</span> | Független: 15 | Függő: 4 | Nem jelölt: 0 | WoS jelölt: 13 | Scopus jelölt: 17 | WoS/Scopus jelölt: 19 | DOI jelölt: 19 </div> </div> </div> </div><div class="JournalArticle Publication long-list">
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<div class="title"><a href="/gui2/?mode=browse¶ms=publication;31612924" target="_blank">AnnotatorJ: an ImageJ plugin to ease hand annotation of cellular compartments</a></div> <div> <span class="journal-title">MOLECULAR BIOLOGY OF THE CELL</span>
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<div class="lastModified">Utolsó módosítás: 2022.07.08. 13:13 Bernátskyné Babus Csilla (SZTE admin4)
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<div class="lockedBy">Ideiglenesen zárolva 2022.09.08. 08:43 Vándor Andrea (VA, admin)
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<pre class="comment" style="margin-top: 0; margin-bottom: 0;"><u>Megjegyzés</u>: Cited By :13
Export Date: 12 July 2022
CODEN: MBCEE
Correspondence Address: Horváth, P.; Synthetic and Systems Biology Unit, Hungary; email: horvath.peter@brc.hu</pre>
</div></div>