ephys_pipeline:2_phys_gui
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ephys_pipeline:2_phys_gui [2022/01/12 14:47] – [Create Excel entries] lukas.schneider | ephys_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) | ||
- | </ | ||
- | Handles are desribed later on in this section | ||
- | Alternatively, | ||
- | <code matlab> | ||
- | phys_gui_working | ||
- | </ | ||
- | \\ A figure will pop up which looks something like this: | ||
- | {{ : | ||
- | 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 " | ||
- | ===== 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 " | ||
- | |||
- | ===== 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 " | ||
- | |||
- | ==== Waveclus pre-clustering settings ==== | ||
- | ^handle^checkbox^Info^ | ||
- | | handles.WC.threshold | ||
- | | handles.WC.StdThrSU | ||
- | | handles.WC.StdThrMU | ||
- | | handles.WC.hp | ||
- | | handles.WC.hpcutoff | ||
- | | handles.WC.lpcutoff | ||
- | | handles.WC.cell_tracking_distance_limit| site dist | maximum electrode distance for concatenation| | ||
- | | handles.WC.remove_ini | ||
- | |||
- | ==== 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, | ||
- | <code matlab> | ||
- | %% defaults | ||
- | handles.RAM = 24; % SYSTEM MEMORY in GB | ||
- | handles.dtyperead = ' | ||
- | handles.dtypewrite = handles.dtyperead; | ||
- | handles.sys = ' | ||
- | handles.rawname = ' | ||
- | handles.blockfile=0; | ||
- | |||
- | % 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; | ||
- | handles.WC.int_factor = 1; % for potential interpolation for more datapoints to classify | ||
- | handles.WC.interpolation =' | ||
- | handles.WC.stdmax = 100; % Artifact rejection threshold in std | ||
- | |||
- | % FEATURE SELECTION | ||
- | handles.WC.features = ' | ||
- | handles.WC.wavelet=' | ||
- | handles.WC.exclusioncrit = ' | ||
- | handles.WC.exclusionthr = 0.9; % features are excluded, until no feature pairs are correlated more than exclusionthr | ||
- | 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; | ||
- | handles.WC.min_clus_abs = 100; % Minimum cluster size number of spikes | ||
- | handles.WC.min_clus_rel = 0.005; | ||
- | 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=' | ||
- | handles.WC.classify_method= ' | ||
- | |||
- | % PLOTTING | ||
- | handles.WC.temp_plot = ' | ||
- | handles.WC.max_spikes2plot = 1000; % maximum number of spikes to plot. | ||
- | handles.WC.max_nrclasses2plot = 8; % not quite sure where this is used | ||
- | </ | ||
- | |||
- | ===== 2) Create Plexon files ===== | ||
- | There are 3 different plexon file types | ||
- | * If you want (or have) to use the online detected snippets, check " | ||
- | * If you first want to Realign your snippets to the minima, check " | ||
- | * If you want to transfer your waveclus presorting to plexon, check " | ||
- | \\ 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 | ||
- | |||
- | |||
- | ===== 2.5) Create plx file entries ===== | ||
- | This step can be used to automatically update the " | ||
- | |||
- | |||
- | ===== 3) 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 " | ||
- | \\ Here you can find the aforementioned option to skip plx files when using waveclus | ||
- | \\ Another option allows you to disregard spikes (if you are only interested in LFPs). No spike sorting fiels will be needed | ||
- | \\ 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, it speeds up the processes immensely. You can also add LFP data at a later point. | ||
- | \\ If you want LFP data to be processed, you can modify the LFP filter settings here: | ||
- | |||
- | ^handle^checkbox^Info^ | ||
- | |handles.LFP.notch_filter1 | Notch1 |first notch (bandstop) filter frequency band| | ||
- | |handles.LFP.notch_filter2 | Notch2 |second notch (bandstop) filter frequency band| | ||
- | |handles.LFP.HP_filter | ||
- | |handles.LFP.LP_bw_filter | ||
- | |handles.LFP.LP_med_filter | LP(median)|median filter low pass " | ||
- | |||
- | |||
- | |||
- | ===== 4) Create Excel entries ===== | ||
- | Check " |
ephys_pipeline/2_phys_gui.1641998866.txt.gz · Last modified: 2022/12/29 07:15 (external edit)