Below you can find detailed information about data generated by our facility instruments. This is provided to support effective data management planning when working with our facility.
Please reach out if you have any questions or cannot find what you need.
CFT
Attribute
Values
Modality
CFT
Instrument
Output file structure
*.tiff stack – each slice in its own dir w/ rgb and flur of all exposure times
Naming convention
Parent folder is named by user in the software
Raw data extensions and size ranges
*.tiff stack, RGB = ~3mb to 25mb per slice, Flur = ~4mb to 7mb per slice
Reconstructed data extensions and size ranges
Flur = *.jp2 = ~6mb per slice per exposure, RGB = *.jpg = ~1.5mb per slice
Metadata extensions and size ranges
.json ~1kb
Software used to generate data
Xerra Controller for Acq and Xerra Recon for Reconstructed
Software used to read and analyze data
VQ and ImageJ or FIJI
Gamma Counter
Attribute
Values
Modality
Gamma Counter
Instrument
Perkin Elmer Wizard 2
Output file structure
ScanID sequential . csv
Naming convention
See above
Raw data extensions and size ranges
.csv – size depending on how much data acquired but generally a few kb and under .5mb
Username initials (defined by user), data and time of acquisition
Raw data extensions and size ranges
.TIF, .PNG (116-461KB)
Reconstructed data extensions and size ranges
Metadata extensions and size ranges
.txt (3-26 KB)
Software used to generate data
Living Image
Software used to read and analyze data
Living Image
microCT
Attribute
Values
Modality
microCT
Instrument
Bruker Skyscan 1276
Output file structure
One folder with one or more subfolders based on user preferences. (some users put all their data from multiple scans in one giant folder), Between 200 and 3600 tif files (raw data, per FOV scanned, so maybe 3-10x this many in some cases), Between 1 and 10000+ image files (reconstructed data, can be tif, bmp, jpg, png, dcm), 1 or 2 log files (one for acquisition, one for reconstruction (optional), .log plain text), 1 bitmap image, 1-N .oog files (log files for subscans when multiple (N) FOV are imaged), 1-100 tif files (leftovers from reconstruction process, names like “mouse_~02_ar3.tif”), Not all users will do reconstruction on the acquisition computer, so those files may not be present., If InstantRecon is used, possibly hundreds of .iif temp files it fails to delete when done), 1-N csv file with x-ray dose information, 0-N .txt files including a suffix like ‘PreviewInfo.txt’, up to one per N FOVs imaged
Naming convention
All names are up to the user.\xa0 Reconstructed files include “rec_00” in the middle. Raw data includes an 8-digit number starting with 00000000.
Raw data extensions and size ranges
.tif ranging from 330kB – 21.2MB
Reconstructed data extensions and size ranges
.tif, .bmp, .jpg, .png, .dcm, 10kB-32MB
Metadata extensions and size ranges
.log, 4kB
Software used to generate data
Skyscan1276.exe (v 1.6), NRecon/GPUrecon (v 1.7.4.2)
Software used to read and analyze data
Anything that can open an image file. ImageJ, Amira, Dragonfly, Amide, OsiriX, VivoQuant, 3D Slicer, Python, Matlab, etc.
MRI
Attribute
Values
Modality
MRI
Instrument
Bruker AV4 BioSpin
Output file structure
Each experiment starts with the date followed by user defined study name.\xa0 Within the experiment folder there are numerical subfolders where each folder is a scan. In a typical scan folder are text files containing meta data about hardware (uxnmr), pulse sequence (method, pulseprogram, specpar), reconstruction (reco), raw image files (2dseq or rawdata.job0) and converted files such as dicom (.dcm)
Naming convention
EnIm1.dcm
Raw data extensions and size ranges
Raw data are in binary formats. 1MB-200MB
Reconstructed data extensions and size ranges
.dcm, 1MB-200MB
Metadata extensions and size ranges
text files with no extension
Software used to generate data
Paravision v2.0
Software used to read and analyze data
Paravision v2.0, Osirix, ImageJ, 3D slicer, Matlab, etc.
Each image acquisition generates one file containing data and metadata. Each series of images goes into a folder. Each study gets a folder that contains series subfolders., Each study folder also always contains a “Measurementinfo.vxml” file, “Study.bak” file, and a “Study.vxml” file.
Naming convention
Default study name as
Below you can find detailed information about data generated by our facility instruments. This is provided to support effective data management planning when working with our facility.Please reach out if you have any questions or cannot find what you need.
shown in lab share: 4-digit year, 2-digit month, 2-digit day, 24-hour time, seconds, (3 digits), Ex. Jan 1st 2023 12:35:35 would be 20230101123535___, Study name can be changed and will be viewable in lab share and w/in analysis and acquisition software, Default series and image name as shown in lab share: 4-digit year, 2-digit month, 2-digit day, 24-hour time, seconds, (3 digits)., Default series name in analysis and acquisition software is a sequentially numbered starting at 1 “Series X”. If series name is edited from default, it will be viewable w/in analysis software. If no image name is given during acquisition, it will be blank w/in analysis and acquisition software. If image is given name during acquisition, it will be viewable w/in analysis and acquisition software.
Raw data extensions and size ranges
Reconstructed data extensions and size ranges
.vxml (357KB – 1KB), .pimg(3253 – 57KB), .mxml (1KB), .3img (16,805KB), .png (608KB), .mxml.1.bak, .bimg (99,289 – 17,674KB), .ekv (240,595KB), .event (2KB), .physio (824KB), .mimg (9,977KB), .vxml.bak (357KB), These are just representative file sizes I found.
