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ephys_pipeline:2_phys_gui [2022/01/12 14:31] – [2) Create Plexon files] lukas.schneiderephys_pipeline:2_phys_gui [2022/03/17 14:08] (current) – removed lukas.schneider
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-====== Phys gui ====== 
-All preprocessing is done by  
-<code matlab> 
-function phys_gui_execute(handles) 
-</code> 
-Handles are desribed later on in this section 
-Alternatively, you can use a GUI by using the command  
-<code matlab> 
-phys_gui_working 
-</code> 
-\\ A figure will pop up which looks something like this: 
-{{ :ephys_pipeline:phys_gui.png |}} 
-Select your monkey from the dropdown menu 
-\\ Select the session folders you want to process after hitting the "Add date from list" button 
-\\ If you hit "Run", phys_gui will do all the preprocessing that you checked (see below) on the selected folders. The box above will remind you of which steps you selected. 
  
-===== 0) Rename folders ===== 
-In later TDT software versions (synapse - setup 3), the folder naming is different. For converting folders recorded with synapse to the old (our standard) folder naming, check the box "RenameSynapseTankNameToOldTankFormat". 
- 
-===== 1) Waveclus pre-clustering ===== 
-If you want to use the waveclus pipeline, you first need to create waveclus sortcodes. You can do so by checking "WCFromBB". Make sure, the electrode_depths file is update for the selected blocks, as this is a requirement for the current WC preprocessing pipeline (see ...). Folders (WC_Block-N) will be created for each block N, and one additional folder (WC) will contain the clustered data, concatenating for each channel separately all blocks where the electrode was in certain range. 
- 
-==== Waveclus pre-clustering settings ==== 
-^handle^checkbox^Info^ 
-| handles.WC.threshold                   | Threshold  | use negative ('neg'), positive ('pos'), or both ('both')| 
-| handles.WC.StdThrSU                    | Std thr SU | (higher) threshold for SU detection in std's of data| 
-| handles.WC.StdThrMU                    | Std thr MU | (lower) threshold for MU detection in std's of data | 
-| handles.WC.hp                          | filter     | filter type for HP - median('med') or butterworth('but')| 
-| handles.WC.hpcutoff                    | HP         | high pass frequency| 
-| handles.WC.lpcutoff                    | LP         | low pass frequency| 
-| handles.WC.cell_tracking_distance_limit| site dist  | maximum electrode distance for concatenation| 
-| handles.WC.remove_ini                  | INI remove | flag to remove ITI before clsutering| 
- 
-==== Additional Waveclus settings ==== 
-For simplicity, some of the potential waveclus settings have been hardcoded inside phys_gui, calling get_WC_settings. 
-\\ However, when you input the handles directly using phys_gui_execute, you can still define them as you like. 
-<code matlab> 
-%% defaults 
-handles.RAM = 24;                           % SYSTEM MEMORY in GB 
-handles.dtyperead = 'single';               % Data TYPE              
-handles.dtypewrite = handles.dtyperead; 
-handles.sys = 'TD';                         % RECORDING SYSTEM 
-handles.rawname = '*.tdtch';                % RAW DATAFILES NAME 
-handles.blockfile=0;                        % not used? 
- 
-% FILTERING: LINE NOISE 
-handles.WC.linenoisecancelation = 0;         % 1 for yes; 0 for no 
-handles.WC.linenoisefrequ = 50;              % Line noise frequency 
-handles.WC.transform_factor = 0.25;          % microVolts per bit for higher accuracy when saved as int16 after filtering; 
-handles.WC.iniartremovel = 1;                % ignore first 40 samples 
- 
-% DETECTION 
-handles.WC.w_pre = 10;                      % N samples for snippet before threshold crossing 
-handles.WC.w_post = 22;                     % N samples for snipept after threshold crossing 
-handles.WC.ref = 0.001;                     % 'Refractory period' in seconds 
-handles.WC.int_factor = 1;                  % for potential interpolation for more datapoints to classify 
-handles.WC.interpolation ='n';              % Interpolationused or not 
-handles.WC.stdmax = 100;                    % Artifact rejection threshold in std 
- 
-% FEATURE SELECTION 
-handles.WC.features = 'wavpcarawtime';     % features to be considered (in any order: wav(elets),pca,raw (datapoints),time,deriv(ates) 
-handles.WC.wavelet='haar';                 % choice of wavelet family for wavelet features 
-handles.WC.exclusioncrit = 'thr';          % this part is weird to me as well, 
-handles.WC.exclusionthr = 0.9;             % features are excluded, until no feature pairs are correlated more than exclusionthr  %def R^2 = 0.80 
-handles.WC.maxinputs = 9;                  % number of feature inputs to the clustering  
-handles.WC.scales = 4;                     % scales for wavelet decomposition 
- 
-% CLUSTERING  
-handles.WC.num_temp = 18;                   % number of temperatures  
-handles.WC.mintemp = 0;                     % minimum temperature 
-handles.WC.maxtemp = 0.18;                  % maximum temperature   
-handles.WC.tempstep = 0.01;                 % temperature step 
-handles.WC.SWCycles = 100;                  % number of montecarlo iterations 
-handles.WC.KNearNeighb = 11;                % number of nearest neighbors 
-handles.WC.max_spikes2cluster = 40000;      % maximum number of spikes to cluster 
-handles.WC.min_clus_abs = 100;              % Minimum cluster size number of spikes 
-handles.WC.min_clus_rel = 0.005;            % Minimum cluster size as fraction of all spikes 
-handles.WC.max_nrclasses = 11;              % Maximum number of clsuters 
-handles.WC.template_sdnum = 5;              % max radius of cluster in std devs. for classifying rest 
-handles.WC.classify_space='features';       % for classifying rest only 
-handles.WC.classify_method= 'linear';       % for classifying rest only 
- 
-% PLOTTING 
-handles.WC.temp_plot = 'log';              % temperature plot in log scale 
-handles.WC.max_spikes2plot = 1000;         % maximum number of spikes to plot. 
-handles.WC.max_nrclasses2plot = 8;         % not quite sure where this is used 
-</code> 
- 
-===== 2) Create Plexon files ===== 
-There are 3 different plexon file types 
-  * If you want (or have) to use the online detected snippets, check "PLXFromSnippets" 
-  * If you first want to Realign your snippets to the minima, check "PLXFromRealignedSnippets" instead.  
-  * If you want to transfer your waveclus presorting to plexon, check "PLXFromWCFromBB". In this case you can alternatively skip the plexon step by checking "directly form WC" in the combine TDT and MP step 
-\\ The two additional options here are  
-  * for taking over WC waveforms to plexon files (keeping the plexon sortcodes) - this was used to counteract a bug where plexon spike resolution in a few cases was terrible 
-  * for creating a TDT sortcode based on plx sorting - this was used in the initial version to then read out snippets with the TDT software 
- 
- 
- 
-===== Combine ephys and behavioral data ===== 
-After you are done with sorting, you can synchronize your recorded data with behavioral data, adding LFP and spike information in the trial structure format that monkeypsych uses. Check "CombineTDTandMP". 
-\\ In order to indicate which type of sorting you want to use, select one option in the "Choose spikes" section 
-\\ "Snippets" uses the sortcodes based on the original snippets 
-\\ "Realigned" uses the sortcodes based on realigned snippets 
-\\ "FromBB" uses the sortcodes based on WC clustered PLX files 
-\\ Choose "none" in case you are only interested in LFP. No spikes will be added to your combined data. 
-\\  
-\\ There is also an option for disregarding LFP. If you select this option, LFP data in the combined file will not be updated (in case it has been processed previously) or completely left out (if it hasn't been processed before). Use this option as long as you are resorting. You can also add LFP dat at a later point. 
- 
- 
-===== Create Excel entries ===== 
-Check "CreateExcelEntries" for creating/updating the automatic sorting sheet of the respective Excel sorting table with the selected data (sessions). Only works after you did all the preceding steps. 
ephys_pipeline/2_phys_gui.1641997895.txt.gz · Last modified: 2022/12/29 07:15 (external edit)