Your browser doesn't support javascript.
loading
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging.
Schapiro, Denis; Sokolov, Artem; Yapp, Clarence; Chen, Yu-An; Muhlich, Jeremy L; Hess, Joshua; Creason, Allison L; Nirmal, Ajit J; Baker, Gregory J; Nariya, Maulik K; Lin, Jia-Ren; Maliga, Zoltan; Jacobson, Connor A; Hodgman, Matthew W; Ruokonen, Juha; Farhi, Samouil L; Abbondanza, Domenic; McKinley, Eliot T; Persson, Daniel; Betts, Courtney; Sivagnanam, Shamilene; Regev, Aviv; Goecks, Jeremy; Coffey, Robert J; Coussens, Lisa M; Santagata, Sandro; Sorger, Peter K.
Afiliación
  • Schapiro D; Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
  • Sokolov A; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
  • Yapp C; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Chen YA; Institute for Computational Biomedicine and Institute of Pathology, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany.
  • Muhlich JL; Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
  • Hess J; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
  • Creason AL; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
  • Nirmal AJ; Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
  • Baker GJ; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
  • Nariya MK; Image and Data Analysis Core, Harvard Medical School, Boston, MA, USA.
  • Lin JR; Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
  • Maliga Z; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
  • Jacobson CA; Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
  • Hodgman MW; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
  • Ruokonen J; Vaccine and Immunotherapy Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
  • Farhi SL; Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA.
  • Abbondanza D; Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
  • McKinley ET; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
  • Persson D; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
  • Betts C; Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
  • Sivagnanam S; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
  • Regev A; Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
  • Goecks J; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
  • Coffey RJ; Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
  • Coussens LM; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
  • Santagata S; Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
  • Sorger PK; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
Nat Methods ; 19(3): 311-315, 2022 03.
Article en En | MEDLINE | ID: mdl-34824477
Highly multiplexed tissue imaging makes detailed molecular analysis of single cells possible in a preserved spatial context. However, reproducible analysis of large multichannel images poses a substantial computational challenge. Here, we describe a modular and open-source computational pipeline, MCMICRO, for performing the sequential steps needed to transform whole-slide images into single-cell data. We demonstrate the use of MCMICRO on tissue and tumor images acquired using multiple imaging platforms, thereby providing a solid foundation for the continued development of tissue imaging software.
Asunto(s)
Texto completo
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Procesamiento de Imagen Asistido por Computador / Neoplasias Tipo de estudio: Diagnostic_studies Límite: Humans Idioma: En Revista: Nat Methods Asunto de la revista: TECNICAS E PROCEDIMENTOS DE LABORATORIO Año: 2022 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Procesamiento de Imagen Asistido por Computador / Neoplasias Tipo de estudio: Diagnostic_studies Límite: Humans Idioma: En Revista: Nat Methods Asunto de la revista: TECNICAS E PROCEDIMENTOS DE LABORATORIO Año: 2022 Tipo del documento: Article País de afiliación: Estados Unidos