Output Files

File Type


Imaging data log files (.tif)

Arbitrary Line Scanning data files (.pmt.dat, .meta.txt, .scnnr.dat)

Reading Line Scanning Data Files

Photostimulation log files (.stim)

Read Photostim Monitor File :ref:

Integration log file (.csv)

ROI Integration (Online Analysis)

Motion Correction log file (.csv)

Motion Correction

Additional Photostimulation Documentation

If the option is enabled to log information in the photostimulation controls window, a .stim file will be created. The photostimulation log file (.stim) contains a sequence of numbers that is parsed into Nx3 array with three variables, the X coordinate, the Y coordinate, and the beam power. The file can be read using the function scanimage.util.readPhotostimMonitorFile(filename).

1out = scanimage.util.readPhotostimMonitorFile('filename')
3% x,y are in reference coordinate space, beam power is in [V], native readout of photo diode
5out.X = phtstimdata(:,1);
6out.Y = phtstimdata(:,2);
7out.Beam = phtstimdata(:,3);

Additional Motion Correction Documentation

If data logging and motion correction are both enabled, a motion correction output file will be generated with a [File name stem] + “_Motion_” + [File counter] filename.

This file will contain the following attributes: timestamp, frameNumber, success, quality, xyMotion, roiUuid, motionMatrix, z, and channel.