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dat_to_nwb_testing.md

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Patchmaster DAT file to NWB testing notes

Remaining questions

  • Is the metadata mapping accurate? Or how should the other values be filled in?
    • A: some metadata was given by the user, but some was the default patchmaster values and may not be accurate (See table below)
  • Q: What data is acquired on each of the channels when there are multiple?
    • A: acquisition channel 1: VC/CC acquisition, acquisition channel 2: measured stimulation
    • A: stimulus channel 1: VC/CC stimulation, stimulus channel 2: delivered force stimulation
    • A: all channels were not always used for the different stimulus series
  • Q: Paper describes recording pre/during/post amiloride, are these separated in the experiment file?
    • A: May not be able to reconstruction exact drug delivery times, added a note to files with drugs to indicate that they may have an effect on the data acquired
  • For files with multiple blocks with the same series label, should these be described differently or are they all the same?
    • A: See the protocol description for the purpose of the initial stimulus blocks

To do items

  • compare plotting output with example figures or data to confirm units and stimulus reconstruction are correct
  • update metadata descriptions once we determine which are user inputs vs default Patchmaster output values
  • add support for "Increment mode - Alternate" stimulus, check reconstruction of RampIVq-2s stimulus
  • convert remaining files

Current metadata mapping

Note: NWB fields with ["value"] indicates that it's a string that's included in the description/notes attribute, not a unique NWB field

Metadata field Metadata unit NWB file field NWB file unit Notes
Cell ID --- subject.subject_id ---
Cell --- subject.description["cell type"] ---
Strain --- subject.genotype ---
I-soln --- notes["Internal solution"] --- I = internal?
E-soln-ctl --- notes["External solution - control"] --- E = external?
E-soln-exp --- notes["External solution - experimental"] --- E = external?
Tc °C notes["Temperature - cell"] need to add c = cell?
Te °C notes["Temperature - enivornment"] need to add e = environment?
Fc* kHz electrode.filtering need to add low pass cutoff? high pass cutoff?
Fs kHz --- ---
Probe --- session_description - probe id --- probe id?
M-VC --- session_description - force amplitude µN force of the probe? M-VC = MEC-VC?
M-CC --- session_description - force amplitude µN force of the probe? M-CC = MEC-CC?
SM-VC --- --- ---
Miv --- --- µN force of the probe?
Vramp control --- ---
Vramp Gd+ --- ---
Rp MΩ electrode.resistance need to convert Rp = pipette resistance?
Rs MΩ electrode.seal need to add Rs = seal resistance?
Cin pF --- --- whole_cell_capacitance_comp? capacitance compensation?
L (Unscaled) cm ---
W (Unscaled) cm ---
A (Unscaled) cm ---
L (Scaled and Corrected) µm subject.description["length"] µm use scaled vs unscaled?
W (Scaled and Corrected) µm subject.description["length"] µm use scaled vs unscaled?
A (Scaled and Corrected) µm subject.description["length"] µm use scaled vs unscaled? A = area?