دورية أكاديمية
Alignment, segmentation and neighborhood analysis in cyclic immunohistochemistry data using CASSATT.
| العنوان: | Alignment, segmentation and neighborhood analysis in cyclic immunohistochemistry data using CASSATT. |
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| المؤلفون: | Brockman AA; Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA., Khurana R; Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA., Bartkowiak T; Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.; Department of Pathology, Microbiology, & Immunology, Nashville, Tennessee, USA., Thomas PL; Department of Microbiology, Immunology & Physiology, School of Medicine, Meharry Medical College, Nashville, Tennessee, USA.; School of Graduate Studies & Research, Meharry Medical College, Nashville, Tennessee, USA., Sivagnanam S; Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon, USA.; Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA., Betts CB; Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon, USA.; Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA., Coussens LM; Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon, USA.; Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA., Lovly CM; School of Graduate Studies & Research, Meharry Medical College, Nashville, Tennessee, USA.; Division of Hematology-Oncology, Department of Medicine, Nashville, Tennessee, USA., Irish JM; Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.; Department of Pathology, Microbiology, & Immunology, Nashville, Tennessee, USA.; Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA., Ihrie RA; Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.; School of Graduate Studies & Research, Meharry Medical College, Nashville, Tennessee, USA.; Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA.; Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA. |
| المصدر: | Cytometry. Part B, Clinical cytometry [Cytometry B Clin Cytom] 2023 Sep; Vol. 104 (5), pp. 344-355. Date of Electronic Publication: 2023 Feb 07. |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't; Research Support, N.I.H., Extramural |
| اللغة: | English |
| بيانات الدورية: | Publisher: Wiley-Liss Country of Publication: United States NLM ID: 101235690 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1552-4957 (Electronic) Linking ISSN: 15524949 NLM ISO Abbreviation: Cytometry B Clin Cytom Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Hoboken, N.J. : Wiley-Liss, c2002- |
| مواضيع طبية MeSH: | Software* , Microscopy*, Humans ; Immunohistochemistry ; Flow Cytometry ; Cell Nucleus ; Image Processing, Computer-Assisted/methods |
| مستخلص: | Cyclic immunohistochemistry (cycIHC) uses sequential rounds of colorimetric immunostaining and imaging for quantitative mapping of location and number of cells of interest. Additionally, cycIHC benefits from the speed and simplicity of brightfield microscopy, making the collection of entire tissue sections and slides possible at a trivial cost compared to other high dimensional imaging modalities. However, large cycIHC datasets currently require an expert data scientist to concatenate separate open-source tools for each step of image pre-processing, registration, and segmentation, or the use of proprietary software. Here, we present a unified and user-friendly pipeline for processing, aligning, and analyzing cycIHC data - Cyclic Analysis of Single-Cell Subsets and Tissue Territories (CASSATT). CASSATT registers scanned slide images across all rounds of staining, segments individual nuclei, and measures marker expression on each detected cell. Beyond straightforward single cell data analysis outputs, CASSATT explores the spatial relationships between cell populations. By calculating the log odds of interaction frequencies between cell populations within tissues and tissue regions, this pipeline helps users identify populations of cells that interact-or do not interact-at frequencies that are greater than those occurring by chance. It also identifies specific neighborhoods of cells based on the assortment of neighboring cell types that surround each cell in the sample. The presence and location of these neighborhoods can be compared across slides or within distinct regions within a tissue. CASSATT is a fully open source workflow tool developed to process cycIHC data and will allow greater utilization of this powerful staining technique. (© 2023 International Clinical Cytometry Society.) |
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| معلومات مُعتمدة: | S21 MD000104 United States MD NIMHD NIH HHS; P30 CA068485 United States CA NCI NIH HHS; R21 HD099367 United States HD NICHD NIH HHS; U01 CA224276 United States CA NCI NIH HHS; U01 CA224012 United States CA NCI NIH HHS; U54 CA217450 United States CA NCI NIH HHS; R01 CA226833 United States CA NCI NIH HHS; S10 OD023475 United States OD NIH HHS; K00 CA212447 United States CA NCI NIH HHS; R01 NS118580 United States NS NINDS NIH HHS; R01 CA223150 United States CA NCI NIH HHS; U2C CA233280 United States CA NCI NIH HHS; UG1 CA233259 United States CA NCI NIH HHS; R01 CA226909 United States CA NCI NIH HHS |
| فهرسة مساهمة: | Keywords: image analysis; imaging; microscopy; multiparameter analysis; multiplexed analyses |
| تواريخ الأحداث: | Date Created: 20230207 Date Completed: 20231023 Latest Revision: 20231102 |
| رمز التحديث: | 20231103 |
| مُعرف محوري في PubMed: | PMC10404643 |
| DOI: | 10.1002/cyto.b.22114 |
| PMID: | 36748312 |
| قاعدة البيانات: | MEDLINE |
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