Automated Cell Identification Methods for Stained Images using FIJI

dc.contributor.advisorSmela, Elisabeth
dc.contributor.advisorAraneda, Ricardo C.
dc.contributor.authorTudor, Robert
dc.contributor.authorVargas Munoz, Laura A.
dc.contributor.authorAnderson, Roy
dc.contributor.authorHaider, Redwan
dc.date.accessioned2025-04-23T16:59:41Z
dc.date.issued2025-04-21
dc.descriptionPoster
dc.description.abstractAccurate identification of stained cells in images is critical for many applications. One of the current methods is manual identification which is time consuming and has risk of human bias. Standard image processing methods consist of basic thresholding and water shedding. However, they struggle with segmenting cells when there are variations in cell morphology, large range of fluorescence intensity, and background artifacts. In addition to false positives and false negatives, errors include overcounting, undercounting, and inaccurate cell areas. In this project, we developed an automated cell counting approach in ImageJ (Fiji) that incorporates a series of optimized image processing steps that include background subtraction, edge detection, and adaptive thresholding. We also investigated using information from Hoechst nuclear staining to assist with segmentation of Calcein-stained images showing cell metabolism. In order to assess the performance of the various approaches, we manually identified cells in a set of challenging images and compared the results of the existing and proposed automated methods. Results show that the method improves throughput and also provides a robust tool for analysis of complex sample images.
dc.description.sponsorshipNational Science Foundation CBET BIOSENS 2316199, EFRI ELiS 2318027, and ExLENT DREEM 2322699
dc.identifierhttps://doi.org/10.13016/skoh-biqt
dc.identifier.urihttp://hdl.handle.net/1903/33851
dc.language.isoen_US
dc.subjectCell Identification Method
dc.subjectFIJI
dc.subjectCalein Stained cells
dc.subjectCell Segmentation
dc.titleAutomated Cell Identification Methods for Stained Images using FIJI
dc.typePresentation

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