Specifying stimulus on off times - galizia-lab/pyview GitHub Wiki

Relevant columns in Measurement List files

The following columns can be used to specify stimulus related information:

  1. StimON: onset in frames
  2. StimONms: onset in ms
  3. StimOFF: offset in frames
  4. StimLen: length in ms
  5. Odour: stimulus name
  6. OConc: stimulus concentration as a logarithm of 10

Validity of combinations

An entry in a column of a measurement list is considered to be specified if the column exists and the entry in the column is not empty. The following table explains how VIEW interprets combination of parameter specification.

Legend: ✅ specified; ❌ not specified, ⭕ irrelevant for current case

StimON StimONms StimOFF StimLen Validity/Interpretation
Stimulus onset taken from 'StimON'
Stimulus onset taken from 'StimONms'
Stimulus onset taken from 'StimON' only when both refer to the same point in time, when interpreted using data sampling period specified in the column 'Cycle'. Otherwise an error is raised
Stimulus offset taken from 'StimLen'
Stimulus offset taken from 'StimOFF'
Stimulus offset taken from 'StimOFF' and value from 'StimLen' is ignored

Multi-stimulus

Starting with version 0.5, rows of measurement lists can contain information about multiple stimuli. The following table provides a few examples how different entries are interpreted.

Legend: ✅ specified; ❌ not specified, ⭕ irrelevant for current case

No. StimON StimONms StimOFF StimLen Odour OConc Validity/Interpretation (Note frames are numbered 0, 1, 2, 3...)
1 25 35 myodor -2 A single odor named 'myodor' was applied at a concentration of $10^{-2}$ starting at frame 25 and ending at frame 35 (both inclusive)
2 25,45 1000 myodor1,myodor2 -2 Two stimuli were applied.

First stimulus was named 'myodor1', its concentration was $10^{-2}$, began at frame 25 and lasted for 1000ms.

Second stimulus was named 'myodor2', its concentration was $10^{-2}$,began at frame 45 and lasted for 1000ms
3 25,45 35,55 myodor1,myodor2 -2 Two stimuli were applied.

First stimulus was named 'myodor1', its concentration was $10^{-2}$, lasted from frame 25 to frame 35 (both inclusive).

Second stimulus was named 'myodor2', its concentration was $10^{-2}$, lasted from frame 45 to frame 55 (both inclusive)
4 25,45 35,55 myodor1 -2,-4 Two stimuli were applied.

First stimulus was named 'myodor1', its concentration was $10^{-2}$, lasted from frame 25 to frame 35 (both inclusive).

Second stimulus was also named 'myodor1', its concentration was $10^{-4}$, lasted from frame 45 to frame 55 (both inclusive)
5 25,45 35, ,1000 myodor1,myodor2 -2 Two stimuli were applied.

First stimulus was named 'myodor1', its concentration was $10^{-2}$, lasted from the 25th frame to the 35th frame.

Second stimulus was also named 'myodor2', its concentration was $10^{-2}$, lasted for 1000ms from the frame 45
6 25,45, ,,15000 1000 myodor1,myodor2,myodor3 -2 Three stimuli were applied.

First stimulus was named 'myodor1', its concentration was $10^{-2}$, lasted for 1000ms starting at the 25th frame.

Second stimulus was named 'myodor2', its concentration was $10^{-2}$, lasted for 1000ms starting at frame 45.

Third stimulus was named 'myodor3', its concentration was $10^{-2}$, lasted for 1000ms starting at 15000ms
7 25,45,65 35,55 myodor1,myodor2 -2 Invalid as 'StimON' indicates three stimuli while others indicate two.

Notes:

  1. If the number of stimuli applied is 'n', then the number of entries in any of the above columns can either be 'n' or 1. If it is 1, the same value is used for all stimuli.
  2. The onsets and offsets of different stimuli can be specified in different ways, as shown in examples 5 and 6 above.
  3. The entry "35," in example 5 above in the column "StimOFF" implies that stimulus offset as a frame number is specified only for the first stimulus and unspecified for the second stimulus.

Features affected:

  1. If StimON, StimOFF, Stim2ON and Stim2OFF are specified in the measurement list, then they are automatically filled in the dialog for transferring data to ILTIS. ILTIS will subsequently highlight these time periods when plotting ROI traces.
  2. When visualizing time traces of components in view-GUI using the button "Visualize GDM traces", periods of stimulus are highlighted in the background of the traces.
  3. When generating movies, the flag mv_markStimulus can be used to add annotations indicating stimulus application. These are added based on the values specified in the measurement list columns above.
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