correct gain for channels - spikeGLX

+bc/+dependencies/SGLX_readMeta.m

@@ -4,7 +4,7 @@
 % Simple class of MATLAB functions deomonstrating
 % how to read and manipulate SpikeGLX meta and binary files.
 % When this file is included in the MATLAB path, the individual methods
-% are called with SGLX_readMeta.<function name>
+% are called with bc.dependencies.SGLX_readMeta.<function name>
 %
 % The most important method in the class is ReadMeta().
 % The functions for reading binary data are not optimized for speed,
@@ -34,13 +34,16 @@
 % utility functions below.
 %
 function [meta] = ReadMeta(binName, path)
-
+    if nargin < 2
+    full_path_meta = binName;
+    else
     % Create the matching metafile name
     [~,name,~] = fileparts(binName);
     metaName = strcat(name, '.meta');
-
+    full_path_meta = fullfile(path, metaName);
+    end
     % Parse ini file into cell entries C{1}{i} = C{2}{i}
-    fid = fopen(fullfile(path, metaName), 'r');
+    fid = fopen(full_path_meta, 'r');
 % -------------------------------------------------------------
 %    Need 'BufSize' adjustment for MATLAB earlier than 2014
 %    C = textscan(fid, '%[^=] = %[^\r\n]', 'BufSize', 32768);
@@ -101,7 +104,7 @@
     % Get channel index of requested digital word dwReq
     switch meta.typeThis
         case 'imec'
-            [AP, LF, SY] = SGLX_readMeta.ChannelCountsIM(meta);
+            [AP, LF, SY] = bc.dependencies.SGLX_readMeta.ChannelCountsIM(meta);
             if SY == 0
                 fprintf('No imec sync channel saved\n');
                 digArray = [];
@@ -110,7 +113,7 @@
                 digCh = AP + LF + dwReq;
             end
         case 'nidq'
-            [MN,MA,XA,DW] = SGLX_readMeta.ChannelCountsNI(meta);
+            [MN,MA,XA,DW] = bc.dependencies.SGLX_readMeta.ChannelCountsNI(meta);
             if dwReq > DW
                 fprintf('Maximum digital word in file = %d\n', DW);
                 digArray = [];
@@ -119,7 +122,7 @@
                 digCh = MN + MA + XA + dwReq;
             end
         case 'obx'
-            [XA,DW,SY] = SGLX_readMeta.ChannelCountsOBX(meta);
+            [XA,DW,SY] = bc.dependencies.SGLX_readMeta.ChannelCountsOBX(meta);
             if dwReq > DW
                 fprintf('Maximum digital word in file = %d\n', DW);
                 digArray = [];
@@ -317,7 +320,7 @@
             APgain = APgain + 1;
         end
     end
-    fI2V = SGLX_readMeta.Int2Volts(meta);
+    fI2V = bc.dependencies.SGLX_readMeta.Int2Volts(meta);
     APChan0_to_uV = 1e6*fI2V/APgain(1);
     if size(LFgain) > 0
         LFChan0_to_uV = 1e6*fI2V/LFgain(1);
@@ -341,12 +344,12 @@
 %
 function dataArray = GainCorrectNI(dataArray, chanList, meta)
 
-    [MN,MA] = SGLX_readMeta.ChannelCountsNI(meta);
-    fI2V = SGLX_readMeta.Int2Volts(meta);
+    [MN,MA] = bc.dependencies.SGLX_readMeta.ChannelCountsNI(meta);
+    fI2V = bc.dependencies.SGLX_readMeta.Int2Volts(meta);
 
     for i = 1:length(chanList)
         j = chanList(i);    % index into timepoint
-        conv = fI2V / SGLX_readMeta.ChanGainNI(j, MN, MA, meta);
+        conv = fI2V / bc.dependencies.SGLX_readMeta.ChanGainNI(j, MN, MA, meta);
         dataArray(j,:) = dataArray(j,:) * conv;
     end
 end % GainCorrectNI
@@ -365,7 +368,7 @@
 %
 function dataArray = GainCorrectOBX(dataArray, chanList, meta)
 
-    fI2V = SGLX_readMeta.Int2Volts(meta);
+    fI2V = bc.dependencies.SGLX_readMeta.Int2Volts(meta);
 
     for i = 1:length(chanList)
         j = chanList(i);    % index into timepoint
@@ -388,13 +391,13 @@
 function dataArray = GainCorrectIM(dataArray, chanList, meta)
 
     % Look up gain with acquired channel ID
-    chans = SGLX_readMeta.OriginalChans(meta);
-    [APgain,LFgain] = SGLX_readMeta.ChanGainsIM(meta);
+    chans = bc.dependencies.SGLX_readMeta.OriginalChans(meta);
+    [APgain,LFgain] = bc.dependencies.SGLX_readMeta.ChanGainsIM(meta);
     nAP = length(APgain);
     nNu = nAP * 2;
 
     % Common conversion factor
-    fI2V = SGLX_readMeta.Int2Volts(meta);
+    fI2V = bc.dependencies.SGLX_readMeta.Int2Volts(meta);
 
     for i = 1:length(chanList)
         j = chanList(i);    % index into timepoint
@@ -421,7 +424,7 @@
                 'EndOfLine', ')' );
 
     nBank = numel(C{1}) + 1;  % bank0/shank0 is at time = 0
-    srate = SGLX_readMeta.SampRate(meta);
+    srate = bc.dependencies.SGLX_readMeta.SampRate(meta);
 
     bankTimes = zeros([nBank,4], "double");
     bankTimes(2:nBank,1) = double(C{1});
@@ -470,6 +473,7 @@ function writeMeta(meta, newPath)
 % streamStr, e.g. 'ap' or 'lf'
 %
 %
+
 function [runName,gateStr,triggerStr,probeStr,streamStr] = parseFileName(fileName)
 
     % Remove extension, if present

+bc/+load/readSpikeGLXMetaFile.m

@@ -13,98 +13,30 @@
 % microvolts
 %
 
-% read meta file
-filetext = fileread(metaFile);
+meta = bc.dependencies.SGLX_readMeta.ReadMeta(metaFile);
 
-% try and get probe type from meta file (imDatPrb_type or imProbeOpt fields)
-expr_scaling = 'imDatPrb_type=*';
-[~, startIndex] = regexp(filetext, expr_scaling);
-if isempty(startIndex) % try second option: there are two different saving conventions
-    expr_scaling = 'imProbeOpt=*';
-    [~, startIndex] = regexp(filetext, expr_scaling);
-end
-if isempty(startIndex) % if still no probe type information is found, use the param value
-    if strcmp(probeType, 'NaN')
-        error(['no probe type found in spikeGLX meta file and no param.probeType specified. ', ...
-            'Edit the param.probeType value in bc_qualityParamValues.'])
-    end
-else
-    endIndex = find(filetext(startIndex:end) == newline, 1, 'first') + startIndex - 2;
-    if isempty(endIndex)
-        endIndex = length(filetext);
-    end
-    probeType = filetext(startIndex+1:endIndex-1);
-end
-
-% get channel map information
-expr_chanMap = 'imRoFile=';
-[~, startIndexChanMap] = regexp(filetext, expr_chanMap);
-expr_afterChanMap = 'imSampRate';
-[~, endIndexChanMap] = regexp(filetext, expr_afterChanMap);
-if isempty(startIndexChanMap) % new convention in new spike glx argh
-    expr_chanMap = 'imroFile=';
-    [~, startIndexChanMap] = regexp(filetext, expr_chanMap);
-    expr_afterChanMap = 'nDataDirs';
-    [~, endIndexChanMap] = regexp(filetext, expr_afterChanMap);
-end
-
-channelMapImro = filetext(startIndexChanMap+1:endIndexChanMap-2-length(expr_afterChanMap));
+% channelMapImro 
+channelMapImro = meta.imRoFile;
 if isempty(channelMapImro) % default was used
     if strcmp(probeType, '0')
         channelMapImro = 'NPtype21_bank0_ref0';
     end
 end
 
-% get bits_encoding
-expr_imMax = 'imMaxInt=';
-[~, startIndeximMax] = regexp(filetext, expr_imMax);
-if isempty(startIndeximMax) % new convention in new spike glx argh
-    if ismember(probeType, {'1', '3', '0', '1020', '1030', '1100', '1120', '1121', '1122', '1123', '1200', '1300', '1110'}) %NP1, NP1-like
-        bits_encoding = 2^10; % 10-bit analog to digital
-    elseif ismember(probeType, {'21', '2003', '2004', '24', '2013', '2014', '2020'}) % NP2, NP2-like
-        bits_encoding = 2^14; % 14-bit analog to digital
-    else
-        error('unrecognized probe type. Check the imDatPrb_type value in your meta file and create a github issue / email us to add support for this probe type')
-    end
-else
-    endIndex = find(filetext(startIndeximMax:end) == newline, 1, 'first') + startIndeximMax - 2;
-    if isempty(endIndex)
-        endIndex = length(filetext);
-    end
-    bits_encoding = str2num(filetext(startIndeximMax+1:endIndex-1));
-end
+% probeType 
+probeType = meta.imDatPrb_type;
 
-% get
-expr_vMax = 'imAiRangeMax =';
-[~, startIndexvMax] = regexp(filetext, expr_vMax);
-if isempty(startIndexvMax) % new convention in new spike glx argh
-    if ismember(probeType, {'1', '3', '0', '1020', '1030', '1100', '1120', '1121', '1122', '1123', '1200', '1300', '1110'}) %NP1, NP2-like
-        Vrange = 1.2e6; % from -0.6 to 0.6 V = 1.2 V = 1.2 e6 microvolts
-    elseif ismember(probeType, {'21', '2003', '2004', '24', '2013', '2014', '2020'}) % NP2, NP2-like
-        Vrange = 1e6; % from -0.5 to 0.5 V = 1 V = 1 e6 microvolts
-    else
-        error('unrecognized probe type. Check the imDatPrb_type value in your meta file and create a github issue / email us to add support for this probe type')
-    end
-else
-    endIndex = find(filetext(startIndexvMax:end) == newline, 1, 'first') + startIndexvMax - 2;
-    if isempty(endIndex)
-        endIndex = length(filetext);
-    end
-    Vrange = 2 * str2num(filetext(startIndexvMax+1:endIndex-1)) * 1e6;
-end
+%% scaling factor 
+% gain 
+gain_allChannels = bc.dependencies.SGLX_readMeta.ChanGainsIM(meta);
+allChannels_index = bc.dependencies.SGLX_readMeta.OriginalChans(meta);
+thisChannel = find(allChannels_index == peakChan);
+thisGain = gain_allChannels(thisChannel);
 
-% gain - QQ read out from table, modify. this could be wrong in some cases.
-%
-if ismember(probeType, {'1', '3', '0', '1020', '1030', '1100', '1120', '1121', '1122', '1123', '1200', '1300', '1110'}) %NP1, NP2-like
-    gain = 500; % 10-bit analog to digital
-elseif ismember(probeType, {'21', '2003', '2004', '24'}) % NP2, NP2-like
-    gain = 80;
-elseif ismember(probeType, {'2013', '2014', '2020'}) % NP2, NP2-like
-    gain = 100; % 14-bit analog to digital
-else
-    error('unrecognized probe type. Check the imDatPrb_type value in your meta file and create a github issue / email us to add support for this probe type')
-end
+% Vrange / bits_encoding 
+fI2V = bc.dependencies.SGLX_readMeta.Int2Volts(meta);
 
 % calculate scaling factor
-scalingFactor = Vrange / bits_encoding / gain;
+scalingFactor = fI2V / thisGain;
+
 end

+bc/+qm/getRawAmplitude.asv

@@ -0,0 +1,42 @@
+function rawAmplitude_uV = getRawAmplitude(rawWaveforms, peakChan, metaFile, probeType, gain_to_uV)
+% JF, Get the amplitude of the mean raw waveform for a unit
+% ------
+% Inputs
+% ------
+% rawWaveforms: nTimePoints × 1 double vector of the mean raw waveform
+%   for one unit in mV
+% metaFileDir: dir structure containing the location of the raw .meta or .oebin file.
+% probeType: optional. only used if you are using spikeGLX *and* the meta
+% file does not contain any probetype field (imDatPrb_type or imProbeOpt)
+% ------
+% Outputs
+% ------
+% rawAmplitude: raw amplitude in microVolts of the mean raw waveform for
+%   this unit
+
+% sanitize inputs
+if nargin < 4 || isempty(probeType)
+    probeType = 'NaN';
+else
+    probeType = num2str(probeType);
+end
+
+% get scaling factor 
+if strcmp(metaFile, 'NaN') == 0
+    if contains(metaFile, 'oebin')
+        % open ephys format
+        scalingFactor = bc.load.readOEMetaFile(metaFile); % single sclaing factor per channel for now 
+    else
+        % spikeGLX format
+        [scalingFactors_all, ~, ~] = bc.load.readSpikeGLXMetaFile(metaFile, probeType);
+        scalingFactor = scalingFactors_all(peakChan);
+    end
+else
+    scalingFactor = gain_to_uV;
+end
+
+    % scale waveforms to get amplitude in microVolts 
+    rawWaveforms = rawWaveforms .* scalingFactor;
+    rawAmplitude_uV = abs(max(rawWaveforms)) + abs(min(rawWaveforms));
+    %rawAmplitude_mV = rawAmplitude_uV ./1000;
+end

+bc/+qm/getRawAmplitude.m

@@ -1,4 +1,4 @@
-function rawAmplitude_uV = getRawAmplitude(rawWaveforms, metaFile, probeType, gain_to_uV)
+function rawAmplitude_uV = getRawAmplitude(rawWaveforms, peakChan, metaFile, probeType, gain_to_uV)
 % JF, Get the amplitude of the mean raw waveform for a unit
 % ------
 % Inputs
@@ -15,7 +15,7 @@
 %   this unit
 
 % sanitize inputs
-if nargin < 3 || isempty(probeType)
+if nargin < 4 || isempty(probeType)
     probeType = 'NaN';
 else
     probeType = num2str(probeType);
@@ -28,6 +28,7 @@
         scalingFactor = bc.load.readOEMetaFile(metaFile);
     else
         % spikeGLX format
+
         [scalingFactor, ~, ~] = bc.load.readSpikeGLXMetaFile(metaFile, probeType);
     end
 else

+bc/+qm/runAllQualityMetrics.asv

@@ -165,8 +165,8 @@ for iUnit = 1:size(uniqueTemplates, 1)
 
     %% amplitude
     if param.extractRaw
-        qMetric.rawAmplitude(iUnit) = bc.qm.getRawAmplitude(rawWaveformsFull(thisUnit, rawWaveformsPeakChan(thisUnit), :), ...
-            param.ephysMetaFile, param.probeType, param.gain_to_uV);
+        qMetric.rawAmplitude(iUnit) = bc.qm.getRawAmplitude(rawWaveformsFull(thisUnit,  rawWaveformsPeakChan(thisUnit), :), ...
+            rawWaveformsPeakChan(thisUnit), param.ephysMetaFile, param.probeType, param.gain_to_uV);
     else
         qMetric.rawAmplitude(iUnit) = NaN;
         qMetric.signalToNoiseRatio(iUnit) = NaN;

+bc/+qm/runAllQualityMetrics.m

@@ -165,8 +165,8 @@
 
     %% amplitude
     if param.extractRaw
-        qMetric.rawAmplitude(iUnit) = bc.qm.getRawAmplitude(rawWaveformsFull(thisUnit, rawWaveformsPeakChan(thisUnit), :), ...
-            param.ephysMetaFile, param.probeType, param.gain_to_uV);
+        qMetric.rawAmplitude(iUnit) = bc.qm.getRawAmplitude(rawWaveformsFull(thisUnit, :, :), ...
+            rawWaveformsPeakChan(thisUnit), param.ephysMetaFile, param.probeType, param.gain_to_uV);
     else
         qMetric.rawAmplitude(iUnit) = NaN;
         qMetric.signalToNoiseRatio(iUnit) = NaN;

README.md

@@ -23,7 +23,7 @@ Below is a flowchart of how bombcell evaluates and classifies each unit:
 
 Bombcell extracts relevant quality metrics to categorize units into four categories: single somatic units, multi-units, noise units and non-somatic units.
 
-Take a look at the MATLAB live script  [`gettingStarted`](https://github.com/Julie-Fabre/bombcell/blob/main/gettingStarted.mlx) or [`bombcell_pipeline`](https://github.com/Julie-Fabre/bombcell/blob/main/pipelines/bombcell_pipeline.m) to see an example workflow and play around with our small toy dataset. You can also take a look at the exercise we prepared for the 2024 Neuropixels course [here](https://github.com/BombCell/Neuropixels_course_2024). 
+Take a look at the MATLAB live script [`gettingStarted`](https://github.com/Julie-Fabre/bombcell/blob/main/gettingStarted.mlx) to see an example workflow and play around with our small toy dataset. You can also take a look at the exercise we prepared for the 2024 Neuropixels course [here](https://github.com/BombCell/Neuropixels_course_2024). 
 
 #### Installation