{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T22:04:42Z","timestamp":1790546682432,"version":"4.1.0"},"reference-count":45,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2019,3,14]],"date-time":"2019-03-14T00:00:00Z","timestamp":1552521600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010665","name":"H2020 Marie Sk\u0142odowska-Curie Actions","doi-asserted-by":"publisher","award":["RENALTRACT ITN project N \u00b0 642937"],"award-info":[{"award-number":["RENALTRACT ITN project N \u00b0 642937"]}],"id":[{"id":"10.13039\/100010665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The zebrafish is being increasingly used in biomedical research and drug discovery to conduct large-scale compound screening. However, there is a lack of accessible methodologies to enable automated imaging and scoring of tissue-specific phenotypes at enhanced resolution. Here, we present the development of an automated imaging pipeline to identify chemical modifiers of glomerular cyst formation in a zebrafish model for human cystic kidney disease. Morpholino-mediated knockdown of intraflagellar transport protein Ift172 in Tg(wt1b:EGFP) embryos was used to induce large glomerular cysts representing a robustly scorable phenotypic readout. Compound-treated embryos were consistently aligned within the cavities of agarose-filled microplates. By interfacing feature detection algorithms with automated microscopy, a smart imaging workflow for detection, centring and zooming in on regions of interests was established, which enabled the automated capturing of standardised higher resolution datasets of pronephric areas. High-content screening datasets were processed and analysed using custom-developed heuristic algorithms implemented in common open-source image analysis software. The workflow enables highly efficient profiling of entire compound libraries and scoring of kidney-specific morphological phenotypes in thousands of zebrafish embryos. The demonstrated toolset covers all the aspects of a complex whole organism screening assay and can be adapted to other organs, specimens or applications.<\/jats:p>","DOI":"10.3390\/ijms20061290","type":"journal-article","created":{"date-parts":[[2019,3,15]],"date-time":"2019-03-15T04:12:09Z","timestamp":1552623129000},"page":"1290","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":30,"title":["A Smart Imaging Workflow for Organ-Specific Screening in a Cystic Kidney Zebrafish Disease Model"],"prefix":"10.3390","volume":"20","author":[{"given":"Gunjan","family":"Pandey","sequence":"first","affiliation":[{"name":"Acquifer is a division of Ditabis, Digital Biomedical Imaging Systems AG, 75179 Pforzheim, Germany"},{"name":"Department of Pediatrics I, University Children\u2019s Hospital Heidelberg, 69120 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jens H.","family":"Westhoff","sequence":"additional","affiliation":[{"name":"Department of Pediatrics I, University Children\u2019s Hospital Heidelberg, 69120 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7564-9937","authenticated-orcid":false,"given":"Franz","family":"Schaefer","sequence":"additional","affiliation":[{"name":"Department of Pediatrics I, University Children\u2019s Hospital Heidelberg, 69120 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jochen","family":"Gehrig","sequence":"additional","affiliation":[{"name":"Acquifer is a division of Ditabis, Digital Biomedical Imaging Systems AG, 75179 Pforzheim, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2019,3,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1038\/nrg2091","article-title":"Animal models of human disease: Zebrafish swim into view","volume":"8","author":"Lieschke","year":"2007","journal-title":"Nat. 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