The associate type guide

What is the meaning of the data in each associate type?

This is a good question that most people who are new to the software ask.  The answer is that there is no super-easy way to figure out what each associate type is, although we are striving to make this easier.  Since I (SDV) spent many years primarily coding for myself, I did not document these types very well.  However, I will try to improve this going forward, by using the following guidelines:
  1. the "owner" should be the name of the .m file that produces the associate; this will allow one to read the code that generated the associate
  2. the "desc" or description field should say a lot about what the measure is
Nevertheless, there are several rules of thumb for interpreting the associate types.

Associate type name rules of thumb

1.  '<stimulus> test' and '<stimulus> resp'

The directory where most stimuli are run are coded as '<stimulus> test', and the average responses that were recorded to each stimulus presentation are coded as '<stimulus> resp'.

For example, 'FineDir test' is commonly used to indicate the directory where data from the "fine direction test" (that is, the direction test run with the finest steps in direction angle and run at the best spatial and temporal frequency), and 'FineDir resp' would contain the stimulus angles that were tested, the average responses and standard deviations and standard errors:

B1 = findassociate(celldata{i},'FineDir test','','')

should give

B1 = 
     type: 'FineDir test'
    owner: 'gratingsheetlet'
     data: 't00039'
     desc: 'FineDir test'


B2 = findassociate(celldata{i},'FineDir resp','','')

should give

B2 = 
     type: 'FineDir resp'
    owner: 'gratingsheetlet'
     data: [1x1 struct]
     desc: ''

2.  Type names like 'SP F0 Ach OT Response curve' or 'TP Ach OT Response curve'

Since about 2007, we have made an effort to standardize some of our associate type names so that responses that are recorded via fundamentally different methods (electrical recordings vs. calcium imaging, for example) or differ only in color (achromatic vs. S-cone driving or ML-cone driving, for example) can use many of the same analysis programs.  When one looks at a list of associates, one may see several items with 'SP F0 Ach OT' in front, or 'TP Ach OT'.

'SP F0 Ach OT Response curve' means this is spiking data ('SP'), it is the F0 component (or the "mean" response, as opposed to a modulated response), the stimulus was achromatic 'Ach', and that it is an orientation tuning curve result ('OT').

The prefixes that are standardized are as follows:
  • 'SP F0'  -- spike data, F0 ("mean" response)
  • 'SP F1'  -- spike data, F1 (the response that is modulated at the stimulus temporal frequency)
  • 'SP F2'  -- spike data, F2 (the response that is modulated at twice the stimulus temporal frequency)
  • 'TP'  -- Two-photon data, in change in fluorescence (that is, ∆F/F)
The colors that are standardized are as follows:
  • 'Ach'  -- Achromatic (black and white)
  • 'S'  -- S-cone-isolating stimulus (tree shrew)
  • 'ML' -- ML-cone-isolating stimulus (tree shrew)
The tuning curve types that are standardized are as follows:
  • 'OT'  -- orientation tuning (includes direction tuning)
  • 'CT'  -- contrast tuning
  • 'SF'  -- spatial frequency tuning
  • 'TF'  -- temporal frequency tuning
  • 'CEDE'  -- color "Dacey" extended, as in Figure 5, Johnson/Van Hooser and Fitzpatrick 2010