nigeLab_Block

Block

"Building-Block" for managing data from single recordings.

Methods

Constructor	doMethods
Block	Auto Cluster Spikes	Behavior Sync	Event Detection	Event Header
	LFP Decimation	Raw Data Conversion	Re-Reference	Spike Detection
	Unit Bandpass Filter	Video Info Extraction	Video Sync

Utility
Get (Completion) Status	Link Data	Set (Completion) Status	Update Parameters

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Constructor

nigeLab.Block

Creates "building-Block" for managing data from single recordings.

• Associated defaults are stored in nigelObj.Pars.Block (at each hierarchical level)
  • Defaults can be configured in ~/+nigeLab/+defaults/Block.m
    • Critically, all name parsing is configured here. Incorrect parsing configuration is the most-common source of errors in constructing/initializing a Block.
    • There are substantial comments and examples in the code comments, look there for more information.
  • Other +defaults may influence the Block constructor:
    • ~/+nigeLab/+defaults/Animal.m (since Block is constructed during Animal constructor)
    • ~/+nigeLab/+defaults/Tank.m (since Block is constructed during Tank constructor)
    • ~/+nigeLab/+defaults/Video.m (since VidStreams flags can affect Block.init during automated parsing/association of Videos and Video-related Streams with the Block)
    • ~/+nigeLab/+defaults/Queue.m (depending on flags set for parallel or remote processing in combination with specifications of Matlab installation on your local machine)

Example Creation of Block Object

% Get second Block from third Animal of the Tank
animalIndex = 3;
blockIndex = 2;
blockObj = tankObj{animalIndex,blockIndex};

% Construct a Block using two UI prompts: 
% 1) Input block file
% 2) Output (Animal) folder that contains the Block
blockObj = nigeLab.Block();
blockObj = nigeLab.Block([]);

% Construct a Block, specifying save location, but select the file from UI
saveLoc = fullfile('savepath','experimentName','tankName','animalName');
blockObj = nigeLab.Block([],saveLoc);

% Construct a Block, skipping the UI
% Note that if a file path produces parsing errors,
% a UI may pop up to request the correct path.
inputFile = fullfile('inpath','tankName','animalName','blockName.rhd'); % Intan RHD
inputFile = fullfile('inpath','tankName','animalName','blockName.rhs'); % Intan RHS
inputFile = fullfile('inpath','tankName','animalName','blockName','blockName.sev'); % TDT
inputFile = fullfile('inpath','tankName','blockName','blockName.sev'); % TDT - also works
saveLoc = fullfile('savepath','experimentName','tankName','animalName');
blockObj = nigeLab.Block(inputFile,saveLoc);

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doMethods

Block.doAutoClustering

Cluster (SPC, K-Means) spikes based on extracted waveform features (PCs, Wavelet Coefficients)

• Overloads superclass method inherited from nigeLab.nigelObj
  • Superclass just iterates on "connected" nigeLab.Tank and nigeLab.Animal objects.
• The following .Fields must have a true value for .Status:
  • Raw (doRawExtraction)
    • Required (indirectly)
  • Filt (doUnitFilter)
    • Required (indirectly)
  • CAR (doReReference)
    • Required (indirectly)
  • Spikes (doSD)
    • Required (indirectly)
  • SpikeFeatures (doSD)
    • Required directly
  • These requirements can be changed in ~/+nigeLab/+defaults/doActions.m
• Associated defaults are in blockObj.Pars.AutoClustering
  • Defaults can be configured in ~/+nigeLab/+defaults/AutoClustering.m
  • For specific clustering algorithms, such as K-Means or SPC, some configurations are located in ``~/+nigeLab/+defaults/+AutoClustering/[methodname].m`

Example Auto-Clustering

blockObj = tankObj{1,2}; % second Block of first Animal in Tank
doAutoClustering(blockObj); % does auto-clustering and saves to diskfiles
linkToData(blockObj); % connect clusters to blockObj in Matlab
% linkToData(blockObj,'Clusters','Sorted'); % should also work, potentially faster

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Block.doBehaviorSync

WIP: Synchronize neural data with behavioral events

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Block.doEventDetection

WIP: Perform automated detection of events determined by .Videos or .Streams

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Block.doEventHeaderExtraction

WIP: Extract Header for use with .scoreVideo method

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Block.doLFPExtraction

Decimate raw signal to facilitate frequency-domain analyses

• Overloads superclass method inherited from nigeLab.nigelObj
  • Superclass just iterates on "connected" nigeLab.Tank and nigeLab.Animal objects.
• The following .Fields to have a true value for .Status:
  • Raw (doRawExtraction)
    • Required (directly)
  • These requirements can be changed in ~/+nigeLab/+defaults/doActions.m
• Associated defaults are in blockObj.Pars.LFP
  • Defaults can be configured in ~/+nigeLab/+defaults/LFP.m

Example LFP Decimation

blockObj = tankObj{2,:}; % All Blocks from the second Animal of the Tank
doLFPExtraction(blockObj); % extracts LFP and saves to diskfiles
linkToData(blockObj); % connect clusters to blockObj in Matlab
% linkToData(blockObj,'LFP'); % should also work, potentially faster

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Block.doRawExtraction

Extract "raw" recorded amplifier and digital stream signals from recording binaries

• Overloads superclass method inherited from nigeLab.nigelObj
  • Superclass just iterates on "connected" nigeLab.Tank and nigeLab.Animal objects.
• Does not require any other fields to be completed before running (by default)
  • This requirement can be changed in ~/+nigeLab/+defaults/doActions.m
• Associated defaults are somewhat disperse; there are not any explicit +defaults elements corresponding to the Raw field per se; however, the main thing is that parsing parameters must be set up in several places. See Block Constructor for more details.
  • Defaults can be configured in ~/+nigeLab/+defaults/Raw.m

Example Raw Data Extraction

animalObj = tankObj{1}; % Returns 1st Animal in Tank
blockObj = animalObj{[2,5]}; % Returns 2nd and 5th block of 1st Animal in Tank
doRawExtraction(blockObj); % extracts Raw data and saves to diskfiles for both Blocks
linkToData(blockObj); % connect raw data to blockObj in Matlab
% linkToData(blockObj,'Raw','DigIO','AnalogIO','Stim','Time',); % should also work

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Block.doReReference

Apply "virtual" common-average subtraction to each probe separately

• Overloads superclass method inherited from nigeLab.nigelObj

  • Superclass just iterates on "connected" nigeLab.Tank and nigeLab.Animal objects.

• The following .Fields must have a true value for .Status:

  • Raw (doRawExtraction)
    • Required (indirectly)
  • Filt (doUnitFilter)
    • Required (directly)
  • These requirements can be changed in ~/+nigeLab/+defaults/doActions.m

• There are currently no associated +defaults for the .CAR field.

Example Re-Referencing

animalObj = tankObj{[1:3]}; % Returns first three Animals in Tank
blockObj = animalObj{:,[2,5]}; % Returns 2nd and 5th block of each Animal in animalObj array (first 3 animals of Tank)
doReReference(blockObj); % extracts Raw data and saves to diskfiles for both Blocks
linkToData(blockObj); % connect raw data to blockObj in Matlab
% linkToData(blockObj,'CAR',); % should also work

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Block.doSD

Detect spikes in the extracellular field potentials and associate compressed sample features

• Overloads superclass method inherited from nigeLab.nigelObj

  • Superclass just iterates on "connected" nigeLab.Tank and nigeLab.Animal objects.

• The following .Fields must have a true value for .Status:

  • Raw (doRawExtraction)
    • Required (indirectly)
  • Filt (doUnitFilter)
    • Required (indirectly)
  • CAR (doReReference)
    • Required (directly)
  • These requirements can be changed in ~/+nigeLab/+defaults/doActions.m

• Associated defaults are in blockObj.Pars.SD

  • Note that these parameters are somewhat confusing due to being associated with a much older version of nigeLab, but will be ported to a less-confusing naming convention at some point.

Example Spike Detection

blockObj = tankObj{:,:}; % Return all blocks from the Tank 
linkToData(blockObj); % connect clusters to blockObj in Matlab
% linkToData(blockObj,'Spikes','SpikeFeatures'); % should also work, potentially faster

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Block.doUnitFilter

Apply "spike-unit" bandpass filter to recorded extracellular field potentials

• Overloads superclass method inherited from nigeLab.nigelObj
  • Superclass just iterates on "connected" nigeLab.Tank and nigeLab.Animal objects.
• The following .Fields to have a true value for .Status:
  • Raw (doRawExtraction)
    • Required (directly)
  • These requirements can be changed in ~/+nigeLab/+defaults/doActions.m
• Associated defaults are in blockObj.Pars.Filt
  • Defaults can be configured in ~/+nigeLab/+defaults/Filt.m

Example Spike Bandpass Filtering

blockObj = tankObj{:,2}; % Second block from all animals in Tank
doUnitFilter(blockObj); % extracts LFP and saves to diskfiles
linkToData(blockObj); % connect clusters to blockObj in Matlab
% linkToData(blockObj,'Filt'); % should also work, potentially faster

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Block.doVidInfoExtraction

WIP: Get basic video-related information prior to performing manual video curation

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Block.doVidSyncExtraction

WIP: Synchronize videos with neurophysiological data record

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Curation

Block.scoreVideo

WIP: Curate and append metadata to individual "trials" or video frames

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Utility

Block.getStatus

Return the completion status of a given .Field

• superclass method inherited from nigeLab.nigelObj

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Block.linkToData

Connect the data saved on the disk to the hierarchical structure

• superclass method inherited from nigeLab.nigelObj

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Block.updateStatus

Update the completion status of a specific .Field

• superclass method inherited from nigeLab.nigelObj

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Block.updateParams

Update some or all of the sub-fields of .Pars

• superclass method inherited from nigeLab.nigelObj

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