Institute of Marine Biology, Biotechnology and Aquaculture - HCMR
MicroCT Services
Lifewatch Account

Metadata

Through the Data Services the user can view the following metadata:

Metadata about Specimen preparation before scanning

Metadata

Definition

Example(s)

preparationEvent ID

A unique identifier for the preparation event.

"specimen-prep-00002"

specimenID

A unique identifier for the specimen in the format: mCT-0000x (where x = incrementing number, always with preceding zeros)

"mCT-00001"

specimenLabel

The original label assigned on the specimen.

"CalanusSt.307 Dorvilleidae CELB-5e-07"

specimenProvider

The person who provided the specimen that will be scanned

"SarahFaulwetter"

providerInstitute

The institution which provided the specimen that will be scanned.

"HCMR"

specimenDescription

A verbatim description of the specimen, which allows  to understand the nature of the specimen at a glance

"Copepod,whole animal"

"Polychaeta,anterior part"

size_mm

The maximum size of specimen that will be scanned

"3mm x 10mm"

preservationMedium

The current preservation medium of the specimen that will be scanned

"96%Ethanol""water""unknown"

Metadata about preparation during scanning

Metadata

Definition

Example(s)

preparationEvent ID

A unique identifier for the preparation event.

"specimen-prep-00001"

contrastEnhancementMethod

The short name of chemicals used for contrast enhancement (staining)

"none""PTA""Iodine"5"HMDS"

protocol

The detailed protocol of the contrast enhancement method can be a reference to a paper

"0.3% PTA in 70% Ethanol""1% Iodine in 96% Ethanol

time-span

The date and time of the duration ofthe preparation (e.g. the staining process) in the format YYYY-MM-DD and HH-MM

"9.30 am 10-10-2012 to 2.00 pm 10-10-2012"

preparationNotes

Any other notes on the specimen preparation process

"2hours""24hours (overnight)""2x30 min""Object was inserted head-down into the pipette"

specimenID

A unique identifier for the specimen in the format: mCT-0000x (where x = incrementing number, always with preceding zeros)

"mCT-00001"

"mCT-00002"

Metadata about scanning event

Metadata

Definition

Example(s)

scanningEvent ID

A unique identifier for the scanning event in a format: scan-0000x (where x=incrementing number)

"scan-00001"

"scan-00002"

scannedPart

The (body) part of the specimen that has been scanned

"whole specimen"

"whole bone"

"anterior part"

scannedBy

The person who performed the scan

"SarahFaulwetter"

"ThanosDalianis"

scanDate

The starting date of the scanning process in the format YYYY-MM-DD

"5/9/2012"

specimenID

A unique identifier for the specimen in the format: mCT-0000x (where x = incrementing number, always with preceding zeros)

"mCT-00001"

"mCT-00002"

producedDatasetID 

A unique identifier for the product (i.e. dataset) of the scanning process

" mCT-0001.zip"

scanningDuration

The duration of the scan in the format HH:MM

"1:25:53 "

sampleHolder

A description of the device that holds the sample

"yellow pipette tip"

"SkyScan plastic tube"

"styrofoam cylinder"

digitalDevice

The model of the Digital Device that was used for the scanning event

"08E01106"

digitalDeviceType

The brand (manufacturer) of the Digital Device that was used for the scanning event

"Skyscann"

voltage_kV

The voltage in kilovolt (kV) used for scanning

"60"

current_uA

The current in µAmpere used for scanning

"200"

filter

The type of filter that used for scanning

"Aluminium"

 

zoom_um

The resolution of the scan in µm (zoom level)

"1,24"

cameraResolution

The camera resolution settings during scanning

"4000"

averaging

The frame averaging value used for scanning

"3"

randomMovement

The random movement value used for scanning

"0"

"10"

360 degrees

The selection of a 360° or 180° rotation for scanning

"180"
"360"

exposureTime_ms

The exposure time in milliseconds used for scanning

"125"

oversizesettings

The number of oversize parts (vertical & horizontal) used for scanning

"2 vertical"

 

scanNotes

Any other notes on the scanning process

"specimen moved during scan"
"scan too dark"

"projection images are missing"

Metadata about Reconstruction Event

Metadata

Definition

Example(s)

reconstructionEvent ID

A unique identifier for the reconstruction event. In the format scan-0000x_rec-0y

"scan-00001_rec-01""scan-00002_rec-01""scan-00040_rec-02"

reconScope

The reason for reconstruction

"first recon""first 3 attempts in very bad quality, noise…""recon into different file format"

reconBy

The person performing the reconstruction

"Sarah Faulwetter"

inputDatasetID

A unique identifier for the input of the reconstruction process

" mCT-0001.zip"

producedDatasetID 

A unique identifier for the product of the reconstruction process

" mCT-0001-recon0001.zip"

reconDate

The date of reconstruction in the format YYYY-MM-DD

"26/4/2012"

reconDuration

The duration of the reconstruction in the format HH:MM

"0:09:10"

reconNotes

Any other notes on the reconstruction process.

"Reconstruction files are absent"

"reconstruction in tiff format"

Metadata about Post Proccessing

Metadata

Definition

Example(s)

postprocessingEventID

A unique identifier for the postprocessing event

"Post Processing 001"

subvolumeID

A unique identifier for the product of the post processing event

"scan-00001_rec-01_voi-01"9"scan-00035_rec-01_voi-01""scan-00051_rec-01_voi-03"

inputDatasetID

A unique identifier for the input (dataset) of the postprocessing process

" mCT-0001-recon0001.zip"

subvolumeCreatedBy

The person who carried out the post processing event

"SarahFaulwetter"

subvolumeNotes

Any other notes concerning the post processing event

"original recon misaligned, was reconstructed again"

"Subvolume used for creating surface
models"

European Regional Development Fund

Virtual Museum of Natural History