Cellomics Unit CNIC (Head of Unit: María Montoya)
OVERVIEW
Cellomics Unit is a core facility which dedicates it’s activity to the two principal cell analytical techniques; flow cytometry and high content screening (HCS) and supports quantitative image-based research. Main tasks at the current employment are management of the Unit’s activities which are:
• Provide state-of-art Core Facility services, training, and support in the field of flow cytometry, high content screening
• Development of advanced image processing and analysis customized solutions.
• Technological innovation and the development of new imaging applications.
• Organization of external and internal international congresses and advanced workshops.
• Scientific research in the field of tumor cell migration and invasion. Research projects range from in vitro studies (function of biomolecules) to tracking biological processes in living cells.
• Pursue independent and collaborative research programs based on extra-mural public/non-profit funding, which would contribute publications and biological and technological development.
The Image Analysis Unit (IAU) has been established within the Cellomics Unit with the aim of providing analysis solutions for image-based scientific applications by developing computational techiniques that extract information from biological images. The image analysis group focuses on the development and validation of novel analysis methods for images coming from different imaging modalities; from advanced optical microscopy to optical tomography. Analysis methods are implemented for resolving molecular/cellular to tissue/organ structures for a broad range of biological imaging applications.
Cellomics Unit is a core facility which dedicates it’s activity to the two principal cell analytical techniques; flow cytometry and high content screening (HCS) and supports quantitative image-based research. Main tasks at the current employment are management of the Unit’s activities which are:
• Provide state-of-art Core Facility services, training, and support in the field of flow cytometry, high content screening
• Development of advanced image processing and analysis customized solutions.
• Technological innovation and the development of new imaging applications.
• Organization of external and internal international congresses and advanced workshops.
• Scientific research in the field of tumor cell migration and invasion. Research projects range from in vitro studies (function of biomolecules) to tracking biological processes in living cells.
• Pursue independent and collaborative research programs based on extra-mural public/non-profit funding, which would contribute publications and biological and technological development.
The Image Analysis Unit (IAU) has been established within the Cellomics Unit with the aim of providing analysis solutions for image-based scientific applications by developing computational techiniques that extract information from biological images. The image analysis group focuses on the development and validation of novel analysis methods for images coming from different imaging modalities; from advanced optical microscopy to optical tomography. Analysis methods are implemented for resolving molecular/cellular to tissue/organ structures for a broad range of biological imaging applications.
Advanced technologies and application development
HCS services which include design, development (miniaturization, automation, analysis) and performance of siRNA library screening. HCS assays developed at the unit include:
• Receptor internalization
• Actin cytoskeleton reorganization
• Focal adhesion organization
• Membrane receptor expression/compartimentalization and colocalization
Specific image analysis application developments include:
• High Content screening: Including well and cell based image analysis to capture the phenotypes of interest (signal intensity, signal colocalization in different cell compartments, morphological descriptors…), quality check, and hit list identification
• 3D and 4D modeling: Including 3D perinuclear region modeling, mathematical statistical shape modelling of embryo herart and quantiifiaction of mitosis orientations by computational geometry and vector calculus
• Image registration : Landmark and elastic registration to correct for capture misalignment
• Computer vision methods : A big range of algorithms to process high dimensional image data, and transform it to numerical and binary descriptors.Machine learning algorithms considering the shape and local texture of individual cells such asgaussian derivatives Gabor and Fourier texture features.
• 2D and 3D image analysis and segmentation: Adherent and suspended cell segmentation, 3D segmentation of heart organ boundary, cells, mitotic spindles, telomeres…
• Machine learning: Clustering, and supervised classification approaches for the recognition of complex cellular phenotypes such as SVMs, KNN...
• Receptor internalization
• Actin cytoskeleton reorganization
• Focal adhesion organization
• Membrane receptor expression/compartimentalization and colocalization
Specific image analysis application developments include:
• High Content screening: Including well and cell based image analysis to capture the phenotypes of interest (signal intensity, signal colocalization in different cell compartments, morphological descriptors…), quality check, and hit list identification
• 3D and 4D modeling: Including 3D perinuclear region modeling, mathematical statistical shape modelling of embryo herart and quantiifiaction of mitosis orientations by computational geometry and vector calculus
• Image registration : Landmark and elastic registration to correct for capture misalignment
• Computer vision methods : A big range of algorithms to process high dimensional image data, and transform it to numerical and binary descriptors.Machine learning algorithms considering the shape and local texture of individual cells such asgaussian derivatives Gabor and Fourier texture features.
• 2D and 3D image analysis and segmentation: Adherent and suspended cell segmentation, 3D segmentation of heart organ boundary, cells, mitotic spindles, telomeres…
• Machine learning: Clustering, and supervised classification approaches for the recognition of complex cellular phenotypes such as SVMs, KNN...
Existing infrastructure capacity
HCS resources include:
• A liquid handling workstation connected to a cell culture incubator with 110 plate throughput (Freedom EVO, Tecan) and a plate storage carrousel with 220 microplate storage capacity.
• An automated confocal microscope for microplate reading (Opera, Perkin Elmer) equiped with a plate handler with 14 position plate shelf and barcode reader.
• Whole genome human and mouse siRNA libraries (4 individual siRNA-oligos per gene. Thermo Scientific).
The Unit is equipped with dedicated image analysis software packages (Acapella, Definiens, MatLab) and develops custom algorithms for image analysis.
• A liquid handling workstation connected to a cell culture incubator with 110 plate throughput (Freedom EVO, Tecan) and a plate storage carrousel with 220 microplate storage capacity.
• An automated confocal microscope for microplate reading (Opera, Perkin Elmer) equiped with a plate handler with 14 position plate shelf and barcode reader.
• Whole genome human and mouse siRNA libraries (4 individual siRNA-oligos per gene. Thermo Scientific).
The Unit is equipped with dedicated image analysis software packages (Acapella, Definiens, MatLab) and develops custom algorithms for image analysis.
Training Activity
Internal courses on Image analysis, general and advanced applied courses on specific image analysis software (Definiens, Acapella)
External courses organized
• 2010: 1st Definiens Users Symposium. CNIC. Madrid. Spain
• 2011: CNIC High Content Screening Workshop. Madrid. Spain
• 2012: Image Cytometry Course. CNIC internal course.
External courses organized
• 2010: 1st Definiens Users Symposium. CNIC. Madrid. Spain
• 2011: CNIC High Content Screening Workshop. Madrid. Spain
• 2012: Image Cytometry Course. CNIC internal course.
Ongoing funded research projects
The Unit conducts research in “Identification of novel molecular players in tumor cell invasion by high content screening”. This project is funded by Fondo de investigaciones Sanitarias FIS. Spanish Science and Innovation Ministry (PS09/01028)
External Collaborations
• CesViMA Supercomputing and Visualization Centre in Madrid. Parque tecnológico. Universidad Politécnica de Madrid.
• Machine learning group. Escuela Politecnica Superior. Universidad Autónoma de Madrid
• REMOA (Spanish Network Advanced Light Microscopy)
• SDDN (Spanish Drug Discovery Network)
• Machine learning group. Escuela Politecnica Superior. Universidad Autónoma de Madrid
• REMOA (Spanish Network Advanced Light Microscopy)
• SDDN (Spanish Drug Discovery Network)
Group
Head of Unit: María Montoya
Support Scientists:
Jose Manuel Ligos (JML)
Hind Azegrouz (HA)
Gopal Karemore (GK)
Technicians:
Raquel Nieto
Mariano Vitón
Irene Palacios
PhD Student: Marco Cordani
PostDoctoral fellow: Silvia Fernandez
The group includes three senior technicians, JML dedicated to flow cytometry and HCS assay development. HA and GK are computer scientists dedicated to image processing algorythm development and implementation of high throughput data analysis workflows. They are in charge of internal users training programmes. Other technicians (RN, MV, and IP) are dedicated to the core facility services on HCS being in charge of robotic platform (MVV), the automatic imaging system (RN/IP) and for the cellular assay (IP/IC). Finally a pHD student and postdoctoral research fellow (SC) carry out scientific research activity.
Support Scientists:
Jose Manuel Ligos (JML)
Hind Azegrouz (HA)
Gopal Karemore (GK)
Technicians:
Raquel Nieto
Mariano Vitón
Irene Palacios
PhD Student: Marco Cordani
PostDoctoral fellow: Silvia Fernandez
The group includes three senior technicians, JML dedicated to flow cytometry and HCS assay development. HA and GK are computer scientists dedicated to image processing algorythm development and implementation of high throughput data analysis workflows. They are in charge of internal users training programmes. Other technicians (RN, MV, and IP) are dedicated to the core facility services on HCS being in charge of robotic platform (MVV), the automatic imaging system (RN/IP) and for the cellular assay (IP/IC). Finally a pHD student and postdoctoral research fellow (SC) carry out scientific research activity.
Publications since 2008
AUTHORS (in order of authorship): J.J. Bravo-Cordero, R. Marrero-Diaz., D. Megías, L.Genis, A. Garcia-Grande, M.A. Garcia, A.G. Arroyo, and M.C. Montoya
TITLE: MT1-MMP proinvasive activity is regulated by a novel Rab8-dependent exocytic pathway
JOURNAL/BOOK TITLE: EMBO J 26:1499-1510.
DATE OF PUBLICATION (*): 2007
AUTHORS (in order of authorship): M. Yañez-Mó, O. Barreiro, P. Gonzalo, A. Batista, D. Megías, L. Genís, N. Sachs, M. Sala-Valdés, M.A. Alonso, M.C. Montoya, A. Sonnenberg, A.G. Arroyo, F. Sánchez-Madrid
TITLE: MT1-MMP collagenolytic activity is regulated through association with tetraspanin CD151 in primary endothelial cells.
JOURNAL/BOOK TITLE: Blood. 112:3217-26
DATE OF PUBLICATION (*): 2008
AUTHORS (in order of authorship): R. Marrero-Diaz, J.J. Bravo-Cordero, D. Megías, M.A.García, R.A. Bartolomé, J. Teixido, and M.C. Montoya
TITLE: Polarized MT1-MMP-CD44 interaction and CD44 cleavage reveal a novel role for MT1-MMP in rear detachment during cell invasion.
JOURNAL/BOOK TITLE: Cell Motil Cytoskeleton 66:48-
DATE OF PUBLICATION (*): 2009
AUTHORS (in order of authorship): M. Martínez-Burgos, L. Herrero, D. Megías, R. Salvanes, M.C. Montoya, A.C. Cobo, J.A. Garcia-Velasco.
TITLE: Vitrification versus slow freezing of oocytes: effects on morphologic appearance, meiotic spindle configuration, and DNA damage.
JOURNAL/BOOK TITLE: Fertil. Steril. 95:374-7
DATE OF PUBLICATION (*): 2010
AUTHORS (in order of authorship): Escobar B, de Cárcer G, Fernández-Miranda G, Cascón A, Bravo-Cordero JJ, Montoya MC, Robledo M, Cañamero M, Malumbres M.
TITLE: Brick1 is an essential regulator of actin cytoskeleton required for embryonic development and cell transformation.
JOURNAL/BOOK TITLE: Cancer Res. 70:9349-59.
DATE OF PUBLICATION (*): 2010
AUTHORS (in order of authorship): A. Echarri, O. Muriel, DM. Pavón, H. Azegrouz, F. Escolar, MC. Terrón, F. Sánchez-Cabo, F. Martínez, M.C. Montoya, O. Llorca and M.A. Del Pozo
TITLE: Caveolar domain organization and trafficking is regulated by Abl kinases and mDia1
JOURNAL/BOOK TITLE: Journal of Cell Science (Epub Ahead of PrintDATE OF PUBLICATION (*): 2012
AUTHORS (in order of authorship): Azegrouz, H., Karemore, G., Torres A., Alaíz, C.M., Gonzalez, A.M., Nevado, P, Pellinen, T., del Pozo, M.A., Dorronsoro, J.R., and Montoya, M.C.
TITLE: “Cell-based imaging- and biology- metrics enhances HCS assay robustness”JOURNAL/BOOK TITLE: In preparation
AUTHORS: Azegrouz, H., Karemore, G., Torres A., Alaíz, C.M., Gonzalez, A.M., Nevado, P, Pellinen, T., del Pozo, M.A., Dorronsoro, J.R., and Montoya, M.C.
TITLE: “Cell-based imaging- and biology- metrics enhances HCS assay robustness”
JOURNAL/BOOK TITLE: Submitted
AUTHORS (in order of authorship): C. Muñoz-Agudo, B. Diez-Cabezas, J.J. Bravo-Cordero, M. Casanova, C. Boullosa, M.C. Guadamillas, I. Ezkurdia, A. Valencia, D. Gonzalez-Pisano, M.A. del Pozo and M.C. Montoya
TITLE: Rab8-mediated Rho GTPase activity and Focal Adhesion Turnover regulates Directional Cell Migration
JOURNAL/BOOK TITLE: In preparation
TITLE: MT1-MMP proinvasive activity is regulated by a novel Rab8-dependent exocytic pathway
JOURNAL/BOOK TITLE: EMBO J 26:1499-1510.
DATE OF PUBLICATION (*): 2007
AUTHORS (in order of authorship): M. Yañez-Mó, O. Barreiro, P. Gonzalo, A. Batista, D. Megías, L. Genís, N. Sachs, M. Sala-Valdés, M.A. Alonso, M.C. Montoya, A. Sonnenberg, A.G. Arroyo, F. Sánchez-Madrid
TITLE: MT1-MMP collagenolytic activity is regulated through association with tetraspanin CD151 in primary endothelial cells.
JOURNAL/BOOK TITLE: Blood. 112:3217-26
DATE OF PUBLICATION (*): 2008
AUTHORS (in order of authorship): R. Marrero-Diaz, J.J. Bravo-Cordero, D. Megías, M.A.García, R.A. Bartolomé, J. Teixido, and M.C. Montoya
TITLE: Polarized MT1-MMP-CD44 interaction and CD44 cleavage reveal a novel role for MT1-MMP in rear detachment during cell invasion.
JOURNAL/BOOK TITLE: Cell Motil Cytoskeleton 66:48-
DATE OF PUBLICATION (*): 2009
AUTHORS (in order of authorship): M. Martínez-Burgos, L. Herrero, D. Megías, R. Salvanes, M.C. Montoya, A.C. Cobo, J.A. Garcia-Velasco.
TITLE: Vitrification versus slow freezing of oocytes: effects on morphologic appearance, meiotic spindle configuration, and DNA damage.
JOURNAL/BOOK TITLE: Fertil. Steril. 95:374-7
DATE OF PUBLICATION (*): 2010
AUTHORS (in order of authorship): Escobar B, de Cárcer G, Fernández-Miranda G, Cascón A, Bravo-Cordero JJ, Montoya MC, Robledo M, Cañamero M, Malumbres M.
TITLE: Brick1 is an essential regulator of actin cytoskeleton required for embryonic development and cell transformation.
JOURNAL/BOOK TITLE: Cancer Res. 70:9349-59.
DATE OF PUBLICATION (*): 2010
AUTHORS (in order of authorship): A. Echarri, O. Muriel, DM. Pavón, H. Azegrouz, F. Escolar, MC. Terrón, F. Sánchez-Cabo, F. Martínez, M.C. Montoya, O. Llorca and M.A. Del Pozo
TITLE: Caveolar domain organization and trafficking is regulated by Abl kinases and mDia1
JOURNAL/BOOK TITLE: Journal of Cell Science (Epub Ahead of PrintDATE OF PUBLICATION (*): 2012
AUTHORS (in order of authorship): Azegrouz, H., Karemore, G., Torres A., Alaíz, C.M., Gonzalez, A.M., Nevado, P, Pellinen, T., del Pozo, M.A., Dorronsoro, J.R., and Montoya, M.C.
TITLE: “Cell-based imaging- and biology- metrics enhances HCS assay robustness”JOURNAL/BOOK TITLE: In preparation
AUTHORS: Azegrouz, H., Karemore, G., Torres A., Alaíz, C.M., Gonzalez, A.M., Nevado, P, Pellinen, T., del Pozo, M.A., Dorronsoro, J.R., and Montoya, M.C.
TITLE: “Cell-based imaging- and biology- metrics enhances HCS assay robustness”
JOURNAL/BOOK TITLE: Submitted
AUTHORS (in order of authorship): C. Muñoz-Agudo, B. Diez-Cabezas, J.J. Bravo-Cordero, M. Casanova, C. Boullosa, M.C. Guadamillas, I. Ezkurdia, A. Valencia, D. Gonzalez-Pisano, M.A. del Pozo and M.C. Montoya
TITLE: Rab8-mediated Rho GTPase activity and Focal Adhesion Turnover regulates Directional Cell Migration
JOURNAL/BOOK TITLE: In preparation