What happens during signal calculation? - galizia-lab/pyview GitHub Wiki

Flag LE_CalcMethod

The flag LE_CalcMethod defines how signals are calculated from the raw data, i.e. how the variable 'sig1' is calculated from 'raw1'. Some are very simple formulas, some more complex. For example, '0' places raw1/1000 into sig1, i.e. scales down raw fluoroscence values. '3' is a plain deltaF/F, '4' a plain ratio. Here is a brief description of the most important value settings for this flag:

  • '0': sig1 = raw1 / 1000
  • '1': sig1 = raw2 / 1000
  • '3': sig1 = deltaF/F0, with background subtraction
  • '4': sig1 = raw1/raw2
  • '3xyy': family of methods to calculate deltaF/F, which includes a filter correcting for lateral light scattering (spatial extent of yy µm), and a bleach and/or noise correction option (x). Use 36yy to enable bleach correction and 39yy to disable bleach correction.
  • '4xyy': family of methods to calculate ratio signals, which includes a filter correcting for lateral light scattering (spatial extent of yy µm), and a bleach and/or noise correction option (x). Use 46yy to enable bleach correction and 49yy to disable bleach correction. If the flag LE_StartBackground is larger than 0, then this family of methods calculates deltaR = R - R0, where R0 is the baseline value of the ratio R=raw1/raw2. R0 is calculated as defined by the flags LE_StartBackground and LE_PrestimEndBackground, as well as the onset of the first stimulus
  • '5xyy': family of methods to calculate corrected raw data, which includes a filter correcting for lateral light scattering (spatial extent of yy µm), and a bleach and/or noise correction option (x). Use 56yy to enable bleach correction and 59yy to disable bleach correction.

Flags affecting calculation of signals

LE_StartBackground

This flag specifies the frame number at the beginning of the interval used for calculating baseline Fluorescence.

LE_PrestimEndBackground

This flag specifies the number of frames between the end of the interval for calculating baseline Fluorescence and the onset of the first stimulus application.

VIEW_ScatterLightFactor

This flag specifies the strength of the filter used to compensate for light scattering. Default value is 1. Value of 0 turns off light scattering compensation irrespective of values of yy specified in the LE_CalcMethod.

NOTE: For correct calculation of baseline Fluorescence, the onset of the first stimulus application has to be correctly set in the measurement list file (guide) in addition to setting these two flags correctly.