Glossary of abbreviations

Global

These abbreviations are used in the project gran proposal and in the central index to find data from the different research groups. Local indices for the different data types will have additional type-specific set of abbreviations.

FDCNS Fluid Dynamics of the Central Nervous System

Research groups

BMC Biomaterials Science Center
TKI Theodor Kocher Institute
TIG The Interface Group

Universities

UNIBA University of Basel
UNIBE University of Bern
UZH University of Zurich

Data types and techniques

CSU-W1 Confocal microscopy
CFD Computational Fluid Dynamics Modeling
2P-IVM Two-photon Microscopy
GRIN Gradient-index lens
IVM Intravital Fluorescence Microscopy
MRI Magnetic Resonance Imaging
NIR Near-infrared imaging
PC-MRI Phase-contrast Magnetic Resonance Imaging
SRµCT Synchrotron Radiation Computed Microtomography

Data descriptors

The metadata table can have different resolutions: For example

  • File_locations tables may have one row per data package or bundles of datasets (e.g., multiple mice)
  • Mice_info tables have one row per mice
  • Scan_list can have one row per folder with scans or one row per reference image files
Data file Each of the individual files that makes a data set
Data set A bundle of files for one mice. One mice can have several data sets (e.g., each is a collection synchrotron images under different conditions)
Data package Collection of data sets collected in one facility for a specific time period (e.g., synchrotron images from Japan in 2023 )
Metadata Data describing data , necessary for reuse and interpretation of the data
Documentation Metadata aimed primarily at being read by humans, e.g., README files, protocols, filenaming conventions, etc
Structured metadata Metadata that can be read by humans and machine, e.g., sidecar files, tables
Tabular metadata Tables with metadata (machine-readable)
JSON JavaScript Object Notation: format of ‘sidecar’ metadata files which are stored next to the data files

Sinergia domain-specific

Pathologies

AD Alzheimer’s Disease
Cerebral amyloid angiopathy CAA
MS Multiple Sclerosis

Mice

arcA𝛽 genetically modified mouse strain, mouse model for Alzheimer’s disease.
EAE Experimental autoimmune encephalomyelitis. Mouse model for multiple sclerosis. Disease is induced via treatment

Biology and physiology

BBB Blood-brain-barrier
BCSFB Blood-cerebrospinal Fluid Barrier
ChP Choroid plexus
CNS Central Nervous System
CSF Cerebrospinal Fluid
EpC Ependymal cilia
ISF Interstitial Fluid
PVS Perivascular spaces
SAS Subarachnoide space

Misc abbreviations

URL Uniform Resource Locato, is the address of a unique resource on the internet.
FOV Field of View
JSON JavaScript Object Notation: format of ‘sidecar’ metadata files
SOP Standard Operating Procedure
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