ESR 14

Comprehensive management of complex data from NHP brain network studies

  • Early Stage Researcher 14 (ESR 14) name:  Reema Gupta

Email address: reema.gupta@lmu.de

Personal Information:

Education: 5 Year Integrated Masters of Science in Physics from Integrated Science Education and Research Centre (ISERC), Visva Bharati University

Publication:

Book Chapter, Nair S.S., Muddapu V.R.J., Sriram M., Aditya R., Gupta R., Chakravarthy S. (2022) Is There a Better Way to Assess Parkinsonian Motor Symptoms?—Experimental and Modelling Approach. In: Arjunan S.P., Kumar D.K. (eds) Techniques for Assessment of Parkinsonism for Diagnosis and Rehabilitation. Series in BioEngineering. Springer, Singapore. https://doi.org/10.1007/978‑981‑16‑3056‑9_10 Awards: INSPIRE Scholarship , Scholarship for Higher Education (SHE) funded by the Department of Science and Technology(DST), India for the period 2015‑2020.

  • Host Institution: Ludwig-Maximilians-Universität München  
  • Supervisors: Prof Dr T. Wachtler   
  • Project title: Comprehensive management of complex data from NHP brain network studies
  • Project description:

Advanced experimental paradigms required to study dynamic brain network function in non-human primates' result in multimodal data of high heterogeneity, complexity and volume. Efficiently managing such data for reproducible, collaborative analysis and re-use requires methods and tools supporting consistent data annotation, data organisation, and workflow documentation (Grewe et al 2011, Zehl et al 2016). In this project, we will develop novel approaches for handling heterogeneous data and complex analysis workflows to enable efficient and reproducible data analysis and data sharing. The project will involve close collaboration with experimental laboratories to harmonize data organization, annotation and develop software tools, compatible with current standards in neuroscience, to support reproducibility and data accessibility according to the FAIR principles.

Contact:email Prof Dr Wachtler

More information:

 

  • Secondments:

(1) Labcorp Early Development Services GmbH, 20/06/2022 to 15/07/2022

The PhD secondment gave the ESR an introduction to working in an industrial setting of a contract research organization (CRO) for multisite regulatory toxicity studies, with a survey of different scientific roles. The secondment involved familiarization with toxicology study standards, data types and compliance frameworks  such as the good laboratory practices (GLP). 

The ESR gained an in-depth understanding of special safety pharmacology studies in the non-human primate animal model, with special emphasis on current regulatory requirements of neurobehaviour assessment for learning and memory. The ESR studied the modified Irwin test, Winconsin general test apparatus (WGTA) and monkey Cambridge neuropsychological test automated battery (mCANTAB). She performed sample sessions on the mCANTB Intellistation, explored the generated data and the established data analysis pipeline.

(2) French National Institute of Health and Medical Research (INSERM), 18/09/2023 to 18/10/2023

The secondment opportunity provided the ESR with comprehensive exposure to neuroimaging data management, emphasizing fMRI studies in non-human primates. The ESR focused on developing methods for effective organization of fMRI data, aligning with current neuroscientific standards and FAIR principles. This included hands-on experience with various neuroimaging data formats like DICOM and NIfTI, and the use of open-source tools such as XNAT and BIDS. Key activities involved managing the In2PrimateBrains fMRI dataset, delivering presentations on neuroimaging data management, and participating in collaborative events at the host institute. The ESR’s skills in data management were further enhanced and demonstrated through the development of a modular data curation pipeline. This secondment significantly contributed to the ESR's understanding of neuroimaging challenges and data management strategies, fostering professional growth and collaborative networking opportunities.

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Reema Gupta(Left, ESR14) and Sameer Manickam(Right, ESR5) at the neuroimaging center, CERMEP PRIMAGE in Lyon, France © 2023 by Reema Gupta is licensed under CC BY-NC-ND 4.0. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/4.0/‌