File format of Allogg ABSS on-line detector raw data (Allogg1)
This document applies to our first generation Allogg device used within-house developed software. The second generation Allogg device is used with software developed by Allogg and it produces a different file format.
The data collected using the Allogg ABSS (Allogg AB, Mariefred, Sweden, http://www.allogg.se/) on-line detectors ("blood pumps") is saved in ASCII files named as *.alg. The format is mainly specified by the manufacturer of the device, except for the header lines, starting with #; these lines are written by in-house programs. These lines must specify at least the date of study in a format shown in the example below, because the applied calibration coefficients are selected based on this date. There should also be a line describing the background activity (cps) on the measurement day.
First line of the data contains the measurement start time as HHMMSS.
The data columns are:
- Count collection end time as seconds from the beginning of the measurement
- Counts at channel x
- Counts at channel y
Example #1: beginning of an on-line detector raw data file
# Protocol: "brainflow" (300 [s] 1000 [ms]) # Discriminators: 60 230 0 # 2004-9-11 # Background on 2004-09-11: 5 [cps] 145524 1.0 2 2 2.0 6 5 3.0 4 4 4.0 6 2 5.0 18 7 6.0 10 3 7.0 15 4 8.0 14 2
Calibration of data
Each measurement line is calibrated to units kBq/ml by following this procedure. Note that this does not contain correction for physical decay or dispersion. Normally, blo2kbq or absscal can be used for this purpose.
- Take the value on 3rd data column (or subtract 3rd from 2nd, if both discriminators are to be used).
- Divide it by measurement duration in seconds (specified in title lines in milliseconds)
- If the background activity was specified in the header lines, subtract it from counts-per-sec value (outcome of the previous step)
- Read the two calibration coefficients from
calibration coefficient file:
- selected detector specific detector-to-gamma counter calibration coefficient: “pump3(HR+)” for *.alg files
- read also the last column, gamma counter-to-pet coefficient, which is common to all on-line detectors
- select calibration that is made just before or on the same day as the blood measurement
- Multiply the two calibration coefficients with each other
- Divide the calibration coefficient by the branching ratio of the radioactive label isotope
- Multiply the count-per-second value from step #3 by the combined calibration coefficient
Sample time for each measurement is calculated by subtracting (measurement duration)/2 (measurement duration is specified in file headers in milliseconds) from the measurement end time (column #1). There are separate instructions for correcting data for the physical decay.
Problems with Allogg ABSS on-line detector raw data
Detector seems to be sensitive to background radioactivity, which must be measured and corrected when working with low count rates.
If sampler was started after PET scan
If Allogg ABSS was accidentally started after the PET scan was started, the sample times, and the start time, can be corrected to the .alg file using absstime.
Created at: 2012-01-31
Updated at: 2016-12-14
Written by: Vesa Oikonen, Tuula Tolvanen