The files that are typically created:
tXXXXX/
---- files placed by the master computer at the onset of data acquisition ----
reference.txt % a file describing the type of records that are present in this directory
---- files placed by the NewStim visual stimulus/sound stimulus package ----
stims.mat % the record of stimulation as recorded by the stimulus computer
stims%N.mat % stimsN.mat, where N can be any integer*
---- files placed by CED Spike2/1401, used for multifunction data acquisition/synchronization ----
filetime.txt % the time when this record was initiated, in Spike2 format (seconds since midnight)
frametimes.txt % a list of frame transition times as detected by Spike2 (in seconds, relative to beginning of recording)
spike2datalog.txt % the text data log from the Spike2 console
spike2data.S2R % the data record that was acquired by Spike2; all other files here are derived from this original
% record (I think...not sure what this is)
spike2data.smr % the data record that was acquired by Spike2; all other files here are derived from this original record
spiketimes_N_00M.txt % contains a list of spike times (relative to the beginning of the Spike2 record) for spike channel
% N and Spike2 cluster number M
stimontimes.txt % stim triggers and numbers as detected by Spike2 (in seconds, relative to beginning of the recording)
stimtimes.txt % stim triggers, stim numbers, and frame transition times as detected by Spike2; each line indicates
% the stim code that was encountered in the first number, the time of stimulus onset in the second number,
% and each subsequent number indicates a data frame trigger time; the time units of this file are seconds with
% respect to the Spike2's recording record onset
traintimes_N.txt % when the FitzLab/VHLab Spike2 scripts are used to generate analog output pulses, this file will
% have a list of the times that output pulses were actually delivered; N will run from 0, 1, ...
% depending upon the number of channels used; in seconds, from start of the recording
twophotontimes.txt % a list of the trigger times generated by the 2-photon, as reported by the Spike2 acquisition system;
% in seconds, from time of Spike2 recording
verticalblanking.txt % a list of vertical blanking refresh times as detected by Spike2 (in seconds, with respect to beginning of Spike2 record)
----files placed manually via Plexon's Offline Sorter program ----
plexonspikes-sp2.txt % An array of spike times clustered from Spike2 data; each row contains
% information from 1 spike. The spike times here are synchronized to Spike2.
% The first item in each row is the channel number; the second item is
% the cluster number; the third item is the spike time in seconds relative
% to the beginning of the recording in the same time units as the Spike2 data files
plexonspikes-lv.txt % An array of spike times clustered from LabView data; each row contains
% information from 1 spike. The spike times here are synchronized to LabView and Spike2.
% The first item in each row is the channel number; the second item is
% the cluster number; the third item is the spike time in seconds relative
% to the beginning of the recording in the same time units as the LabView data files
plexonspikes.txt*** % An array of spike times; each row contains information from 1 spike.
% The first item in each row is the channel number; the second item is
% the cluster number; the third item is the spike time in seconds relative
% to the beginning of the Plexon recording
stimtimes_plexon.txt* % File sometimes created when the user is using plexon; this is a text file that contains exported event data
---- files placed by VHLab LabView multichannel data acquisition script ----
vhlvanaloginput.vlh % header file (text, human readable) describing channels that were acquired, sampling rate, etc
% can be read with Matlab function readvhlvdatafile
vhlvanaloginput.vld % data file containing multichannel data samples
% can be opened with Matlab function readvhlvheaderfile
vhlv_filtermap.txt % text file that describes how channels should be arranged for filtering and threshold detection
% can be read with Matlab function loadStructArray
vhlv_thresholds.txt % text file that describes the spike thresholds to be used on each channel for detecting spikes
% can be read with Matlab function loadStructArray
vhlv_channelgrouping.txt% text file that describes how channels should be arranged for the purpose of distinguishing spikes
% can be read with Matlab function loadStructArray
vhlv_syncchannel.txt* % text file that indicates which LabView channel (1..NumChannels) is the sync channel.
% If this file is not present, the sync channel is assumed to be the last channel.
% *Must be made manually if the last channel is the not the sync channel.
---- files placed by our analysis software for LabView multichannel data ----
lv_spikewaveforms_N.vsw % Binary structure with extracted spike waveforms from channel group N in this directory
% can be read with Matlab function readvhlspikewaveformfile
lv_spiketimes_N.vst % Single precision data (float32) with the time of each spike in lv_spikewaveforms_N
lv_spiketimes_N.txt % Contains a list of spike times (relative to the beginning of the LabView record) for channel group N
lv_st_NAME_REF_00M.txt % The spike times of the sorted spikes from name/ref NAME/REF, cluster number M.
% When these clusters are imported, 50 is added to them to distinguish them from the spike2 clusters
lv_ci_NAME_REF_00M.mat % The cluster sorted spikes from name/ref NAME/REF, cluster number M.
% Includes things like mean waveform, quality designation, etc
---- files placed by our software for auditing Spike2 spike clustering ----
spike2matlabclusters_N.vsw % Spike waveforms for all clusters for spike channel group N
spike2matlabclusters_N.mat % Other information (cluster id, times) for the spike waveforms for spike channel group N
---- files placed by PrairieView 2-photon acquisition software ----
% The PrairieView software likes to store its files in DIRNAME-00N, where N increases as more data is collected
% To deal with this, we have PrairieView store its files in tXXXXX-00N at the same level as tXXXXX
tXXXXX-00N/(Prairie image files in TIFF format; header file in XML format)
---- files placed by VHLabs 2-photon analysis software ----
driftcorrect % .mat file with driftcorrection values for each frame
tXXXXX/ % (we're back to the tXXXXX directory now; only PrairieView above writes to the -00N location)
---- files placed by VHLab LabView Intrinsic imaging data acquisition script ----
[TO BE DOCUMENTED] % [DO BE DOCUMENTED]
----files placed by the Intan demo board acquisition program ----
ANYNAME.rhd % An rhd data file. The name doesn't matter, but there has to be a single file.
In the root directory:
associate_variables.tx % a tab-delimited list of associate variables to add to each cell (see help associate_variables_txt)tunitquality.txt % description of single or multi-unit quality (see help unitquality)
unitquality_channelshift.txt % Single number that describes shift between Plexon channels and reference.txt entries
testdirinfo.txt % Describes which txxxxx directories correspond to which stimulation types (see help file)
trainingtype.txt % A single string that describes the type of training that was employed (see help trainingtype)
trainingangle.txt% A text file with the angle (unidirectional or flash) or angles (bidirectional training) that were used
trainingtemporalfrequency.txt% A text file with the temporal frequency used for training
trainingstim.txt % A text file describing the stimulus type used for training (for scrambled stims)
Files that can be created under some circumstances:
When our Spike2 or LabView code cannot find what it thinks is the correct directory for writing its files, it has a backup plan. It writes its data to a directory that is named for the HOUR, MINUTE, and SECOND of the time of acquisition or saving. It is important to quickly move these files to the correct tXXXXX directory.
*** still under development