Files created by vhlabtools and other devices we use before/during acquisition


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
                   %    *must be made manually

----  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.

HR-MN-SEC/
[usual files]


*** still under development

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