Update all codebooks

webpage_contents/experiments/synchrotron_microCT/Mouse_list_codebook.csv

@@ -28,5 +28,5 @@ Artificial_ventilation,Artificial ventilation used (e.g. tracheotomy; intubation
 Research_group_institution,University affiliation of the group(s) who collected the data. (Unibas = University of Basel; Unibe = University of Bern; UZH = University of Zurich)
 Research_group,Abbreviation describing the group(s) who collected the data. (BMC = Biomaterials Science Center; TKI = Theodor Kocher Institute; TIG = The Interface Group)
 Table_date_csv_export,Date of exporting the .xlsx table used for editing to .csv for upload to the FABRIC4 Portal.
-Abbreviation,N/A: Not applicable
-Abbreviation,Unavailable: This information has not been collected
+N/A,Not applicable
+Unavailable,This information has not been collected

webpage_contents/experiments/synchrotron_microCT/Scan_list_codebook.csv

@@ -55,5 +55,5 @@ Disk_Zurich_Physical_Location,Description of the physical location of the harddi
 Research_group_institution,University affiliation of the group(s) who collected the data. (Unibas = University of Basel; Unibe = University of Bern; UZH = University of Zurich)
 Research_group,Abbreviation describing the group(s) who collected the data. (BMC = Biomaterials Science Center; TKI = Theodor Kocher Institute; TIG = The Interface Group)
 Table_date_csv_export,Date of exporting the .xlsx table used for editing to .csv for upload to the FABRIC4 Portal.
-Abbreviation,N/A: Not applicable
-Abbreviation,Unavailable: This information has not been collected
+N/A,Not applicable
+Unavailable,This information has not been collected

webpage_contents/experiments/synchrotron_microCT/beamtimes_codebook.csv

-Variable_name,Description,Description_abbreviation
-Year,Year  from AFFORD project in which activities took place,
-Partner,AFFORD partner team (TIG: the interface group; CRS: Center for Reproducible Science),
-Collaborator,Surname of the main person(s) executing the actions,
-Facility_1,country where data were collected,
-Facility_2,name of synchrotron facility,
-Facility_country,name of experimental facilities of a synchrotron particle accelerator,
-Acquisition_start_date,"DD-MM-YYYY date of the official first day of the beamtime allocated for the experiment. Internally within the Sinergia project, beamtime experiments are often informally identified by the month and year they took place.",
-Acquisition_proposal_number,Identification number of the synchrotron beamtime proposal. This number helps identifying the beamtime experiment at the different facilities,
-Acquisition_data_type,"Contains a shorthand for the scientific purpose for which the data was collected. Typically corresponds to the official project associated with a given beamtime experiment, or is given as ""General""",
-Execution_period,"Whether the activite was conducted before, during (offsite or onsite) or after data acquisition ",
-Purpose,"Goals of the task; Data Sharing and Publishing: open research data  and metadata curation,  documentation and publishing; Internal Documentation:  Activities related to documenting data internally, minimum curation for internal sharing; Data and File Management: file operations and internal documentation that would need to be done even if no data publication was envisioned;  Data Stewardship: helping other groups or researchers setting up similar activities; Supporting Documentation : writing more generic documentation on how-to perform some actions; ",
-Action,Specific actions performed,
-Action_sub,Sub action when applicable (else N/A),
-Description,Free text describing details about the activity ,
-Comments,Free text describing details about the activity ,
-Active_time_h,"Time needed for task spent in action, requiring active work by a person",
-Waiting_time_h,"Time needed for task that does not include any active work from project partners. Most commonly computer busy time (e.g. waiting for file transfer, processing etc.), but may also include waiting for external parties (e.g. IT support)",
-Time_monitoring,"prospective: start of task was anticipated and time tracking was started, giving precise time information. Retrospective: action was already finished when time requirement was calculated, giving only rough estimates",
-Abbreviation,arcAbeta," genetically modified mouse strain, model for Alzheimer's"
-Abbreviation,EtOH, ethanol
-Abbreviation,BMC," Biomaterials Science Center, Sinergia partner in Basel under Prof. Bert Müller"
-Abbreviation,TKI," Theodor-Kocher-Institute, Sinergia partner in Bern under Prof. Britta Engelhardt or Steven Proulx"
-Abbreviation,EAE," Experimental autoimmune encephalomyelitis, an animal model for multiple sclerosis"
-Abbreviation,CSF, cerebrospinal fluid
-Abbreviation,TiB," Tebibyte. unit of data storage equal to 2^40 or 1,099,511,627,776 bytes"
-Abbreviation,BIDS, brain imaging data structure - a metadata standard for neuroimaging data of multiple modalities
-Abbreviation,SHA256, hash functions computed with eight 32-bit words
-Abbreviation,N/A, not applicable
+Variable_name,Description
+Facility_institution,Name or acronym of any overarching organization hosting the facility used for data acquisition (e.g. university hosting core facility; radiation research organization)
+Facility_country,Country where the facility is located
+Facility_name,Name or acronym of the facility used for data acquisition (e.g. core facility; synchrotron)
+Facility_subunit,Name or acronym of the subunit of the facility used for data acquisition (e.g. beamline of a synchrotron)
+Beamtime_start_date,Date of the first official day of the synchrotron beamtime allocation. This does not include any days prior of official beamtime start used for preparation. Format YYYY-MM-DD
+Beamtime_proposal_number,Official proposal number assigned by the synchrotron to the allocated beamtime. This should correspond the number used in the synchrotron databases etc.
+Beamtime_project_description,Shorthand description of the research question investigated during this experiment
+Preparation,"Indicator whether the experiment was in vivo, ex vivo, post mortem or peri mortem"
+Number_of_samples,Number of samples imaged during the beamtime experiment (e.g. number of animals; number of tissues)
+Mean_photon_energy,Mean photon energy of the X-ray beam
+Monochromator,Type of monochromator used for narrowing the energy spectrum of the X-ray beam
+Effective_voxel_size,Effective voxel size of the data. This value derives from the lens magnification and Detector_pixel_size. It is usually measured independently for validation
+Projections_width_in_pixel,Width of the acquired X-ray projection in pixels
+Projections_height_in_pixel,Height of the acquired X-ray projection in pixels
+Field_of_View_width,Width of the acquired X-ray projection in millimeters
+Field_of_View_height,Height of the acquired X-ray projection in millimeters
+Exposure_time,Amount of time that the camera chip used in the X-ray detector setup is exposed to light and collecting photons
+Overhead_time_per_projection,Additional amount of time required on top of the exposure time for the complete acquisition of an X-ray projection (e.g. for readout or rotation stage movements)
+Number_of_projections,The number of X-ray projections collected at multiple angles for the purposes of tomographic reconstruction
+Stage_rotation_angle_range,Indicates the angle the rotation stage was rotated during the full scans. Typical values are 180 ° and 360 °
+Propagation_distance,Distance between the detector and the sample. This value has impacts the amount of edge enhancement seen in the X-ray images
+Detector_model,Name identifying the camera used in the detector setup
+Detector_pixel_size,Pixel size of the physical pixels on the camera chip without magnification
+Detector_width_in_pixel,Width of the camera chip array in number of pixels. This reflects the technical specifications of the camera chip and not the number of pixels used in imaging
+Detector_height_in_pixel,Height of the camera chip array in number of pixels. This reflects the technical specifications of the camera chip and not the number of pixels used in imaging
+Lens_type,Type of lens used for magnification of visible light in the X-ray detector setup
+Lens_f-number,The f-number of a camera lens used for magnification in the X-ray detector setup. Indicated as N/A for microscope objectives where the numerical aperture is provided instead
+Lens_numerical_aperture,The numerical aperture of a microscope objective used for magnification in the X-ray detector setup. Indicated as N/A for camera lenses where the f-number is provided instead
+Scintillator,Material and thickness of the scintillator used to convert X-rays to visible light in the X-ray detector setup
+Radiation_dose_rate,Radiation dose rate measured or estimated for in vivo experiments. This metric is not measured for ex vivo or post mortem experiments
+Table_date_csv_export,Date of exporting the .xlsx table used for editing to .csv for upload to the FABRIC4 Portal.
+N/A,Not applicable
+Unavailable,This information has not been collected
+Variable,This information is different for different scans within the beamtime session. It is provided in this table for overview purposes only