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Identification

Personal identification

Full name
Maria Mafalda Vieira Pereira Gonçalves de Sousa

Citation names

  • Sousa M

Author identifiers

Ciência ID
EF16-257F-7F49
ORCID iD
0000-0003-2238-1070
Education
Degree Classification
2019/02/02 - 2019/02/07
Concluded
 Advanced Training School for BioImage Analysts (Outros)
Major in Image Analysis
Neubias Cost Action, Belgium
2016/09/01 - 2018/07/30
Attended
 Master in Informatics Engineering - Software engineering (Mestrado)
Major in Software engineering
Instituto Politécnico do Porto Instituto Superior de Engenharia do Porto, Portugal
"NA" (THESIS/DISSERTATION)
 15
2018/07/03 - 2018/07/04
Concluded
 Imaris training course for Facility Staff (Curso de Especialização Tecnológica)
Major in Image Analysis
Instituto Gulbenkian de Ciência, Portugal
2015/02 - 2015/03
Concluded
 FELASA B (Outros)
Major in Biologia
Universidade do Porto Instituto de Biologia Molecular e Celular, Portugal
2010/01/01 - 2014/12/03
Concluded
 Doctoral Program in Neuroscience (Doutoramento)
Major in Computational Neuroscience
Universidade do Porto Faculdade de Medicina, Portugal
"Construction And Analysis Of Detailedbiophysical Models For Drt And Lamina I neurones" (THESIS/DISSERTATION)
 Approved with distinction
2012/08/20 - 2012/08/24
Concluded
 Neuron course (Postgraduate Certificate)
Major in Computational Neuroscience
Institute of Science and Technology Austria, Austria
 2 ECTS
2006/10 - 2007/02
Concluded
 Curso livre de Inglês B2.1 (Outros)
Major in Línguas
Universidade do Porto Faculdade de Letras, Portugal
 17
2003/10 - 2006/09
Concluded
 Computational Methods in Science and Engineering (Mestrado)
Major in Computer science and mathematics
Universidade do Porto Faculdade de Engenharia, Portugal
"Probabilistic Methods in Hierarchical Classification: Computational Implementation" (THESIS/DISSERTATION)
 Very good
2005/09/12 - 2005/09/13
Concluded
 Curso de Formação de Monitores do Projecto FEUP 2005/2006 (Outros)
Universidade do Porto Faculdade de Engenharia, Portugal
2005/06 - 2005/06
Concluded
 Formação pedagógica de monitores (Outros)
Major in Ensino
Universidade do Porto, Portugal
1999/09 - 2003/07
Concluded
 Mathematics Applied to Technology (Licenciatura)
Major in Mathematics; Statistics; Modulation; Programming; Signal Processing; Data Analysis;
Universidade do Porto Faculdade de Ciências, Portugal
"Modelação e Simulação do Electrocardiograma a partir de técnicas de simulação e estatística." (THESIS/DISSERTATION)
 14
Affiliation

Science

Category
Host institution 		Employer
2018/04/01 - 2021/03/31 Contracted Researcher (Research) Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2015/10/01 - 2018/03/31 Postdoc (Research) Universidade do Porto Instituto de Biologia Molecular e Celular, Portugal
Universidade do Porto Faculdade de Medicina, Portugal
2014/09/24 - 2015/09/30 Researcher (Research) Universidade do Porto Faculdade de Medicina, Portugal
Universidade do Porto Faculdade de Medicina, Portugal
2008/01/01 - 2009/12/31 Researcher (Research) Universidade do Porto Instituto de Biologia Molecular e Celular, Portugal
2006/01/01 - 2006/12/31 Researcher (Research) Instituto Nacional de Engenharia Biomédica, Portugal
2004/03/01 - 2004/10/01 Research Trainee (Research) Serviço de Bioestatistica e Informática Médica do Porto FMUP, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2017/01/01 - 2021/03/31 Invited Assistant (University Teacher) Universidade do Porto Faculdade de Medicina, Portugal
Universidade do Porto Faculdade de Medicina, Portugal
2010/11/22 - 2011/09/15 Invited Assistant (Polytechnic Teacher) Escola Superior Gestão e Tecnologia do Instituto Politécnico de Viana do Castelo., Portugal

Other Careers

Category
Host institution 		Employer
2021/04/04 - 2023/04/30 Especialista de Informática Grau 3 Nível 2 (Especialista de informática) LabOrders, Portugal

Others

Category
Host institution 		Employer
2023/08/01 - Current Operations coordinator (freelancer) Grand Circle Corporation, United States
2007/05 - 2007/12 Operador de CallCenter MEO Serviços de Comunicações e Multimédia SA, Portugal
2005/07/01 - 2005/07/31 Monitor Universidade do Porto, Portugal
Universidade do Porto, Portugal
2005/02/01 - 2005/07/01 Monitor Universidade do Porto Faculdade de Ciências, Portugal
Universidade do Porto Faculdade de Ciências, Portugal
Projects

Grant

Designation Funders
2016/05/01 - 2018/03/31 Development of an integral solution for biomedical research combining continuous analysis of depth-sensor imaging, neurophysiology and optogenetic stimulation.
Projecto NORTE-01-0145-FEDER-000008
Post-doc Fellow
Concluded
2010/01/01 - 2014/06 Construction And Analysis Of Detailed biophysical Models For Drt And Lamina I neurones
SFRH/BD/60690/2009
PhD Student Fellow
Associação para a Inovação e Desenvolvimento da FCT, Portugal
 Associação para a Inovação e Desenvolvimento da FCT
Concluded
2007/07 - 2010/06 Theoretical models of nociceptive information processing and transmission in the spinal cord´s dorsal horn.
68929
Provided by PTCRIS: 68929
 Fundação para a Ciência e a Tecnologia, I.P.
2006/01/01 - 2006/12/31 Segmentation and Alignment of Medical Images
Projecto INEB/Unidade 174/LSI/2005
Research Fellow
Instituto Nacional de Engenharia Biomédica, Portugal
Concluded

Contract

Designation Funders
2021/02 - Current Defragmentation: bringing BioImage Analysts to the cloud!
Financiado sem Ref
Principal investigator
The Francis Crick Institute, United Kingdom
Ongoing
2018/04/01 - Current Portuguese Platform of BioImaging
PPBI-POCI-01-0145-FEDER-022122
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
 Associação para a Inovação e Desenvolvimento da FCT
Ongoing
2020 - 2020 Integrated Network of European Bioimage Analysis Core Facilities for Open Access Services to Life Scientists (BIASCores)
Não Financiado
Researcher
Cancelled
2019 - 2019 Deep learning on microscopy image analysis: a step forward on current methods
Não Financiado
Principal investigator
Associação para a Inovação e Desenvolvimento da FCT, Portugal
Cancelled
2018 - 2018 Bioimaging software tools and computational infrastructure
Não Financiado
Principal investigator
Cancelled
Outputs

Publications

Conference abstract
  1. Sousa, Maria. "Netbuilder: A Tool for Constructing Large and Complex Neural Networks.". 2009.
    10.3389/conf.neuro.01.2009.11.068
Conference paper
  1. Sousa, Maria. "Reduction in inhibitory control is sufficient to generate hyperalgesia in a spiking model of nociceptive integration in the superficial dorsal horn". 2013.
    10.1186/1471-2202-14-S1-P1
  2. Sousa, Maria. "Analysis of the mechanisms underlying windup using a detailed biophysical model of WDR neurons". 2010.
    Published • 10.1186/1471-2202-11-S1-O14
Conference poster
  1. Rodrigues, Daniela; Tiago Gaspar; Sampaio, Paula; Sousa M. Corresponding author: Rodrigues, Daniela. "Quantitative morphological characterization of pancreatic islets in HE stained slides". Paper presented in ECDP2021, 2021.
    https://doi.org/10.6084/m9.figshare.18737153.v1
  2. Sousa M. "Pancreatic islet segmentation workflow in hematoxylin and eosin stained sections". Paper presented in SPAOM, 2020.
  3. Sousa M. "FRET ratiometric tool: imageJ script.". Paper presented in 4th NEUBIAS Conference & Symposium Bordeaux, 2020.
    https://doi.org/10.7490/f1000research.1117828.1
Journal article
  1. Joana Bravo; Inês Ribeiro; Ana Filipa Terceiro; Elva B. Andrade; Camila Cabral Portugal ; Igor M. Lopes ; Maria Azevedo; et al. Corresponding author: Summavielle, Teresa. "Neuron-microglia contact dependent mechanisms attenuate methamphetamine-induced microglia reactivity and enhance neuronal plasticity". Cells 11 3 (2022): https://www.mdpi.com/2073-4409/11/3/355.
    Open access • Accepted • https://doi.org/10.3390/cells11030355
  2. Raquel Pinto; Ana Magalhães; Sousa M; Pedro Barros ; Gomes, João F. R.. Corresponding author: Gomes, João F. R.. "Translation of transient mouse stroke model to clinical practice: from surgery upgrade to behavioral functional workflow". (2022):
    Submitted
  3. Sousa, Mafalda; Corrà, Marta Francisca; Reis, Inês; Tanganelli, Fabiana; Vila-Chã, Nuno; Sousa, Ana Paula; Magalhães, Rui; et al. "Advantages of an Automated Method Compared With Manual Methods for the Quantification of Intraepidermal Nerve Fiber in Skin Biopsy". Journal of Neuropathology & Experimental Neurology (2021): http://dx.doi.org/10.1093/jnen/nlab045.
    Open access • Published • 10.1093/jnen/nlab045
  4. Salazar, Maria J; Rodrigues, Adriana R; Sousa, Mafalda; Magalhães, José; Neves, Delminda; Almeida, Henrique; Gouveia, Alexandra M. "Characterization of a-MSH browning effect in diverse mice white adipose tissue depots". Journal of Molecular Endocrinology 66 1 (2021): 23-34. http://dx.doi.org/10.1530/jme-20-0002.
    10.1530/jme-20-0002
  5. Rocha, Maria Inês; Dias, Filipa; Resende, Mariana; Sousa, Mafalda; Duarte, Margarida; Tomás, Ana Maria; Castro, Helena. "Leishmania infantum Enhances Migration of Macrophages via a Phosphoinositide 3-Kinase ¿-Dependent Pathway". ACS Infectious Diseases 6 7 (2020): 1643-1649. http://dx.doi.org/10.1021/acsinfecdis.0c00080.
    Published • 10.1021/acsinfecdis.0c00080
  6. Pádua, Diana; Barros, Rita; Amaral, Ana Luísa; Mesquita, Patrícia; Freire, Ana Filipa; Sousa, Mafalda; Maia, André Filipe; et al. "A SOX2 Reporter System Identifies Gastric Cancer Stem-Like Cells Sensitive to Monensin". Cancers 12 2 (2020): 495. http://dx.doi.org/10.3390/cancers12020495.
    Open access • Published • 10.3390/cancers12020495
  7. Pereira, António; Sousa, Mafalda; Almeida, Ana C.; Ferreira, Luísa T.; Costa, Ana Rita; Novais-Cruz, Marco; Ferrás, Cristina; et al. "Coherent-hybrid STED: high contrast sub-diffraction imaging using a bi-vortex depletion beam". Optics Express 27 6 (2019): 8092. http://dx.doi.org/10.1364/oe.27.008092.
    Open access • 10.1364/oe.27.008092
  8. Sousa M; Szucs P; Lima D; Aguiar P. "The pronociceptive dorsal reticular nucleus contains mostly tonic neurons and shows a high prevalence of spontaneous activity in block preparation.". (2014): http://europepmc.org/abstract/med/24431401.
    10.1152/jn.00440.2013
  9. Sousa, Mafalda; Aguiar, Paulo. "Building, simulating and visualizing large spiking neural networks with NeuralSyns". Neurocomputing 123 (2014): 372-380. http://dx.doi.org/10.1016/j.neucom.2013.07.034.
    Published • 10.1016/j.neucom.2013.07.034
  10. Cardoso-Cruz H; Sousa M; Vieira JB; Lima D; Galhardo V. "Prefrontal cortex and mediodorsal thalamus reduced connectivity is associated with spatial working memory impairment in rats with inflammatory pain.". (2013): http://europepmc.org/abstract/med/23872106.
    10.1016/j.pain.2013.07.020
  11. Aguiar, Paulo; Sousa, Mafalda; Szucs, Peter. "Versatile Morphometric Analysis and Visualization of the Three-Dimensional Structure of Neurons". Neuroinformatics 11 4 (2013): 393-403. http://dx.doi.org/10.1007/s12021-013-9188-z.
    Published • 10.1007/s12021-013-9188-z
  12. Mafalda Sousa; Peter Szucs; Paulo Aguiar. "Reduction in inhibitory control is sufficient to generate hyperalgesia in a spiking model of nociceptive integration in the superficial dorsal horn". BMC Neuroscience 14 Suppl 1 (2013): P1-P1. http://dx.doi.org/10.1186/1471-2202-14-s1-p1.
    Published • 10.1186/1471-2202-14-s1-p1
  13. Aguiar P; Sousa M; Lima D. "NMDA channels together with L-type calcium currents and calcium-activated nonspecific cationic currents are sufficient to generate windup in WDR neurons.". (2010): http://europepmc.org/abstract/med/20554833.
    10.1152/jn.00834.2009
  14. Paulo Aguiar; Mafalda Sousa; Deolinda Lima. "Analysis of the mechanisms underlying windup using a detailed biophysical model of WDR neurons". BMC Neuroscience 11 Suppl 1 (2010): O14-O14. http://dx.doi.org/10.1186/1471-2202-11-s1-o14.
    Published • 10.1186/1471-2202-11-s1-o14
Journal issue
  1. Sousa M; Maria Manuel Azevedo. "Peer Review Report For: ContactJ: Lipid droplets-mitochondria contacts characterization through fluorescence microscopy and image analysis". F1000Research 10 263 (2021): https://f1000research.com/articles/10-263/v1#referee-response-82672.
    Under revision • https://doi.org/10.5256/f1000research.55111.r82672) • Editor
Newsletter article
  1. Sousa M. "StarDist: Application of the deep-learning tool for phase-contrast cell images. My favourite image analysis tool", Wiley Analytical Science, 2020, https://analyticalscience.wiley.com/do/10.1002/was.000400090/full/.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2020/02 BioImage Analysis Facility Management Example Neubias Satellite Meeting
Neubias (Luxemburgo, Luxembourg)
2013/11 The electrophysiological properties of a pronociceptive nucleus: Dorsal Reticular Nucleus. The 10th International Medical Postgraduate Conference
Charles University in Hradec Kralove (Hradec Králové , Czech Republic)
2013/06 Reduction in inhibitory control is sufficient to generate hyperalgesia in a spiking model of nociceptive integration in the superficial dorsal horn. Nociceptive Processing In The Uncharted Spinal Dorsal Horn
Neuroscience Workshop FMUP (Porto, Portugal)
2012/05 Models for nociceptive information processing. Mathematical Neuroscience Workshop
CMUP (porto, Portugal)
2007/02 Probabilistic Methods of Hierarchical Classification: Computational Implementation Jornadas de Classificação e Análise de Dados
Instituto Superior Engenharia do Porto – Instituto Politécnico do Porto (po, Portugal)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2017/01 - 2017/09 Pathological Anatomy final course project - animal behaviour in a chronic pain model
Co-supervisor
 Anatomia Patológica, Citológica e Tanatológica (Degree)
Instituto Politécnico do Porto Escola Superior de Saúde, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2019/10 - 2019/10 Neubias Training Schools, Porto 2019 COST Action http://eubias.org/NEUBIAS/training-schools/staff/ts13-porto-2019/ (2019/10)
Meeting (Member of the Scientific Committee)
 Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal

Instituto de Engenharia de Sistemas e Computadores Tecnologia e Ciência, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2021/11 - 2021/11 SPAOM is a joint effort from Red Española de Microscopía Óptica Avanzada (REMOA) and the Portuguese Platform of Biomedical Imaging (PPBI), to organise an annual congress covering new applications in optical microscopy and image analysis.
Congress
 SPAOM 2021
Instituto Gulbenkian de Ciência, Portugal
2020/03/03 - 2020/03/06 4th Neubias Satellite meeting talk, Bordeus 2020 http://eubias.org/NEUBIAS/neubias2020-conference/bordeaux-2020/program-bordeaux-2020/
Conference
 4th Neubias Conference
2019/11/06 - 2019/11/08 SPAOM 2019 Spanish & Portuguese Advanced Optical Microscopy
Congress
 SPAOM
Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
2019/02/06 - 2019/02/08 3rd NEUBIAS Conference
Conference
 3rd NEUBIAS Conference
2019/02/02 - 2019/02/07 NEUBIAS 2019 Training School #11 BioImage Analysts
Meeting
 Neubias Training Schools

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2021/04/23 Development of Bioimage Analysis tools for the study of neurogenesis and neurodegeneration
(Thesis) Main arguer
 PAU CARRILLO BARBERA (PhD)
Universitat de València, Spain
2020/06/08 Development of image analysis tools for the characterization of astrocytic calcium waves in controlled electrophysiological conditions
(Thesis) Main arguer
 Leonor Sá (Master)
Universidade do Porto Faculdade de Engenharia, Portugal

Association member

Society Organization name Role
2013 - 2017 Sociedade Portuguesa de Neurociências Associate Member
2013 - 2014 Organization for Computational Neurosciences Association member

Committee member

Activity description
Role 		Institution / Organization
2019 - Current NEUBIAS Academy is a new initiative, aimed to provide sustainable material and activities focused on Training in Bioimage Analysis.
Member
 Neubias Cost Action, Belgium

Conference scientific committee

Conference name Conference host
2021/11/21 - 2021/11/25 SPAOM IGC

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2020/01/01 - Current BioImage Analysis (18h) Mestrado em Neurobiologia (Outros) Universidade do Porto Faculdade de Medicina, Portugal
2019 - Current Course on Optical Microscopy Imaging for Biosciences. An annual training course of 5 days at I3S Course on Optical Microscopy Imaging for Biosciences (Outros) Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2019 - Current Digital Image Analysis, Optical Microscopy Imaging for Biosciences annual course Optical Microscopy Imaging for Biosciences Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2018/09 - Current Introduction to digital bioimage analysis, annual training course at I3S of 3 days (Outros) Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2021/10 - 2021/10 EMBO Practical Course aims at a multidisciplinary approach to the study of molecular interactions from and in biological systems, integrating biochemical/biophysical methodologies with live cell microscopy techniques. Biomolecular interaction analysis: From molecules to cells Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2021/05 - 2021/05 BioImage Analysis for High Content Screening. An annual training course at I3S BioImage Analysis for High Content Screening (Outros) Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2019/10/14 - 2019/10/17 Image segmentation Neubias Training School for Facility Staff (Curso de Especialização Tecnológica) Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal

Instituto de Engenharia de Sistemas e Computadores Tecnologia e Ciência, Portugal
2019/04 - 2019/10 BIA Workflows - a series of 2h workshops about image analysis (Outros) Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2017/01 - 2019/07/30 Neuroscience In-silico (14h discipline) Mestrado em Neurobiologia (Mestrado) Universidade do Porto Faculdade de Medicina, Portugal
2010/11/22 - 2011/09/15 Análise Matemática (teórico-praticas 1 semestre) Licenciatura Engenharia Informática (Licenciatura) Escola Superior Gestão e Tecnologia do Instituto Politécnico de Viana do Castelo., Portugal
2010/11/22 - 2011/09/15 Análise Matemática Licenciatura em Engenharia Alimentar (Licenciatura)
2011/01 - 2011/07 Cálculo Infinitésimal (teórico praticas 1 semestre) Licenciatura em Gestão (Licenciatura) Instituto Politécnico de Viana do Castelo, Portugal
2005/07/01 - 2005/07/31 Bola de Cristal versus Estatística - Universidade Júnior Universidade Junior (160h) (Ensino básico 2º ciclo)
2003/10/01 - 2003/10/31 Matemática 12º ano (38h) Projecto FEUP MAFIQUI (Outros) Universidade do Porto Faculdade de Engenharia, Portugal
2003/03/23 - 2003/07/15 Métodos Estatístisco (praticas 1 semestre) (Licenciatura) Universidade do Porto Faculdade de Ciências, Portugal
2003/03/23 - 2003/07/15 Investigação Operacional e Delineamento de Experiências (praticas 1 semestre) (Licenciatura) Universidade do Porto Faculdade de Ciências, Portugal

Journal scientific committee

Journal title (ISSN) Publisher
2021/04 - 2021/04 F1000Research ( 2046-1402)
2019/12 - 2019/12 Machine Vision and Applications Springer
2018 - 2018 Microscopy Research and Technique (1059-910X) Wiley Online Library
Distinctions

Award

2019 Cost Action Grant for the participation of Neubias Training Schools
Neubias Cost Action, Belgium

Other distinction

2012 Honorable mention. Best poster presentation in the 2nd FMUP Doctoral Students Meeting
Universidade do Porto Faculdade de Medicina, Portugal
2012 Travel award to FENS Forum