Glossary of abbreviations

Global

These abbreviations are used in the project grant 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

UNIBAS 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 make up a data set
Data set A bundle of files for one mouse. One mouse can have several data sets (e.g., each is a collection of 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
CAA Cerebral amyloid angiopathy
MS Multiple Sclerosis
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

Synchrotron computed tomography imaging

Abbreviation Full expression Explanation
Beamtime Beamtime is assigned competitively
Detector
TiB Tebibyte unit of data storage equal to 2^40 or 1,099,511,627,776 bytes
TB Terabyte unit of data storage equal to 10^12 or 1,000,000,000,000 bytes. It is often imprecisely used to refer to tebibytes, most egregiously by operating system software, leading to common incorrect usage
GiB Gibibyte unit of data storage equal to 2^30 bytes
GB Gigabyte unit of data storage equal to 10^9 or 1,000,000,000 bytes. It is often imprecisely used to refer to gibibytes, most egregiously by operating system software, leading to common incorrect usage
MiB Mebibyte unit of data storage equal to 2^20 bytes
MB Megabyte unit of data storage equal to 10^6 or 1,000,000 bytes. It is often imprecisely used to refer to mebibytes, most egregiously by operating system software, leading to common incorrect usage
BIDS Brain imaging data structure a metadata standard for neuroimaging data of multiple modalities
SHA256 Secure Hash Algorithm 256 Cryptographic hash function computed with eight 32-bit words. In this project, this algorithm is used to calculate checksums that allow for identifying changes in data such as data corruption.
Checksum A checksum is a small-sized block of data derived from another block of digital data for the purpose of detecting errors that may have been introduced during its transmission or storage. By themselves, checksums are often used to verify data integrity but are not relied upon to verify data authenticity.
Synchrotron Particle accelerator for electrons, used to generate X-rays with very high photon flux and spatial and temporal coherence.
SRµCT synchrotron radiation computed mictrotomography Computed microtomography using synchrotron radiation as X-ray source
ANSTO Australian Nuclear Science & Technology Organisation Umbrella organization running particle accelerators and nuclear reactors in Australia
AS Australian Synchrotron Synchrotron in Melbourne, Victoria, Australia
CLS Canadian Light Source Synchrotron in Saskatoon, Saskatchewan, Canada
DESY Deutsches Elektronen-Synchrotron Umbrella organization running synchrotrons in Germany. Historically, the name referred to a specific synchrotron that is no longer in operation. Colloquially, this name is used to refer to the PETRA III synchrotron.
PETRA III Positron–Electron Tandem Ring Accelerator Synchrotron in Hamburg, Germany
DLS Diamond Light Source Synchrotron in Didcot, Oxfordshire, United Kingdom
ESRF European Synchrotron Radiation Facility Synchrotron in Grenoble, France
PSI Paul Scherrer Institut Umbrella organization running the Swiss Light Source and other particle accelerators in Switzerland. Colloquially, this name is sometimes used to refer to the SLS synchrotron.
SLS Swiss Light Source Synchrotron in Villigen, Aargau, Switzerland
SOLEIL Source optimisée de lumière d’énergie intermédiaire du LURE (Laboratoire pour l’utilisation du rayonnement électromagnétique) Synchrotron in Gif-sur-Yvette, Île-de-France, France
SPring-8 Super Photon Ring – 8 GeV Synchrotron in Sayō, Hyōgo, Japan
BL Beamline Experimental endstation making use of synchrotron radiation coming from a storage ring. Multiple beamlines can be built for a single storage ring, allowing for multiple, highly varied experiments with a single synchrotron particle accelerator
IMBL Imaging and Medical Beam Line Computed microtomography beamline at the Australian Synchrotron.
BMIT Biomedical Imaging and Therapy Computed microtomography beamline at the Canadian Light Source
P05 P05 - Imaging Beamline Computed microtomography beamline at the Deutsches Elektronen Synchrotron, for lower photon energies < 50 keV
P07 P07 - The High Energy Materials Science Beamline of Helmholtz-Zentrum Hereon and DESY Computed microtomography beamline at the Deutsches Elektronen Synchrotron, for higher photon energies > 50 keV
I13-2 The Diamond Manchester Imaging Branchline Computed microtomography beamline at the Diamond Light Source
ID17 ID17 - Biomedical Beamline Computed microtomography beamline at the European Synchrotron Radiation Facility. Permanently closed down for computed microtomography experiments since July 2022.
ID19 ID19 - Microtomography beamline Computed microtomography beamline at the European Synchrotron Radiation Facility
TOMCAT Beamline for TOmographic Microscopy and Coherent rAdiology experimentTs Computed microtomography beamline at the Swiss Light Source
ANATOMIX Advanced Nanotomography and Imaging with coherent X rays Computed microtomography beamline at the Source optimisée de lumière d’énergie intermédiaire du LURE
BL20B2 BL20B2 Medical and Imaging I beamline Computed microtomography beamline at the Super Photon Ring – 8 GeV
Beamtime Access to synchrotrons for experiments is given to researchers for a specific amount of time during specific, pre-assigned dates. Both the duration and the specific time slots may be referred to as beamtime
Beamtime proposal Access to synchrotrons for experiments is limited due to the demand for beamtime exceeding the available supply. Unpaid, scientific access to synchrotrons is therefore assigned competitively based on experimental proposals, which are typically evaluated by a scientific committee and assigned beamtime based on their relative ranking.
Beamtime proposal number Experimental proposals to receive beamtime at a synchrotron are always assigned an internal number by the respective synchrotron for their internal tracking. This number is frequently also used in the Synchrotron file system or databases
User Term used to refer to researchers who are external to a synchrotron facility, but have received beamtime and are performing experiments there.

Misc abbreviations

URL Uniform Resource Locator, 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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