ephys_pipeline:4_meta-info
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ephys_pipeline:4_meta-info [2022/01/11 19:15] – lukas.schneider | ephys_pipeline:4_meta-info [2022/03/17 14:09] (current) – removed lukas.schneider | ||
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- | ====== Meta-info ====== | ||
- | Meta-info is information not stored in the respective data files directly, | ||
- | like electrode location, unit_IDs, SNR/ | ||
- | |||
- | ===== electrode_depths file ===== | ||
- | |||
- | Find/create the electrode depth file corresponding to your monkey in the following location: \\ C: | ||
- | \\ It should look like this: | ||
- | <code matlab> | ||
- | k=0; | ||
- | k=k+1; Session{k}=20150508; | ||
- | k=k+1; Session{k}=20150508; | ||
- | k=k+1; Session{k}=20150508; | ||
- | </ | ||
- | Note that here each BLOCK has one line, channels | ||
- | ===== same_cells file ===== | ||
- | |||
- | Find/create the same cells file corresponding to your monkey in the following location: \\ C: | ||
- | \\ It should look like this: | ||
- | <code matlab> | ||
- | k=0; | ||
- | k=k+1; Session{k}=20150508; | ||
- | k=k+1; Session{k}=20150513; | ||
- | k=k+1; Session{k}=20150514; | ||
- | </ | ||
- | Note that here each CELL has one line, channel is unique per line, sortcodes correspond to blocks. The same cell might be assigned to different sortcodes in different blocks. | ||
- | **Importantly, | ||
- | ===== sorted_neurons table ===== | ||
- | |||
- | Find/create the Sorted neurons excel table corresponding to your monkey in the following location: | ||
- | C: | ||
- | (replace username with your username, Monkey with the monkey' | ||
- | |||
- | There are two main sheets in this excel file: | ||
- | * automatic_sorting | ||
- | * final_sorting | ||
- | The idea is, that a large part of the information can be updated automatically (**see...**), | ||
- | For both sheets, each line represents one unit recorded in one block (and run) AND/OR the corresponding LFP site | ||
- | |||
- | ==== Automatically created entries ==== | ||
- | ^Monkey ^Session ^Date ^Run ^Block ^Chan ^z ^Unit ^N_spk ^Neuron_ID ^Site_ID ^Times_same_unit ^ | ||
- | | Lin | 1 | 2010508 | 3 | 1 | 1 |15000|a|15251|Lin_20150508_01|Lin_20150508_Site_01|1| | ||
- | | Lin | 1 | 2010508 | 4 | 2 | 1 |15000|a|15251|Lin_20150508_01|Lin_20150508_Site_01|1| | ||
- | |||
- | * Monkey: monkey initials (first 3 letters) | ||
- | * Session: A session counter (irrelevant, | ||
- | * Date: Date of recording | ||
- | * Run: Corresponding behavioral run | ||
- | * Block: ephys recording block | ||
- | * Chan: electrode number (channel) | ||
- | * z: Electrode depth (from guide tube tip) - taken from [[ephys_pipeline: | ||
- | * Unit: sortcode assigned to this cell (a=first, | ||
- | * N_spk: Total spike count | ||
- | * Neuron_ID: Cell identifier (the [[ephys_pipeline: | ||
- | * Site_ID: LFP site identifier (Based on electrode depth, same site can be recorded in different blocks and at the same time with different units) | ||
- | * Times_same_unit: | ||
- | |||
- | ==== Manually added entries ==== | ||
- | ^SNR_rank ^Single_rank ^Stability_rank ^Set ^Target ^Hemisphere ^Grid ^x ^y ^ | ||
- | | 1 | 1 | 0 | 1 | dPul|left|22.5|-5|8| | ||
- | | 3 | 2 | 1 | 1 | dPul|left|22.5|-5|8| | ||
- | |||
- | The first three entries should be taken from your notes during sorting. | ||
- | * SNR_rank: Signal to noise ratio assessment (1 - best SNR to 3 - marginal SNR) | ||
- | * Single_rank: | ||
- | * Stability_rank: | ||
- | |||
- | The other entries typically don't change within a session and can be taken from the handwritten log (notes taken during recording, to be found in Y: | ||
- | * Set: Dataset, relevant for assigning to specific project (see [[ephys_pipeline: | ||
- | * Target: Area | ||
- | * Hemisphere: left/right | ||
- | * Grid: grid identifier (diameter.number) | ||
- | * x: grid hole coordinate x | ||
- | * y: grid hole coordinate y | ||
- | |||
- | ==== Electrode travel ==== | ||
- | Last, but not least, there is another entry which is typically calculated inside the table using different approaches per experimenter: | ||
- | |||
- | ==== Dataset convention ==== | ||
- | |||
- | ^ Numeric code ^ Meaning ^ | ||
- | |General notes |Neuron set IDs with no decimals correspond to the ones in which the task had the desired characteristics for a given dataset, e.g. set =2 gaze modulation with 3 initial starting locations 15° horizontal eccentricity and 10° vertical eccentricity; | ||
- | |Additional notes |when unit ID has a termination " | ||
- | |1| Direct-visually- and memory-guided saccade dataset| | ||
- | |2| Gaze modulation dataset, i.e. memory saccades, rectangular grid of targets starting at -15°, 0°, +15°| | ||
- | |2.1| Memory saccades center-out / out-center 12° and 24° eccentricity (blocked per run)| | ||
- | |2.2| Memory saccades center-out & out-center 12° and 24° eccentricity (interleaved in the same run)| | ||
- | |2.3| Memory saccades, rectangular grid of targets starting at -12°, 0°, +12°, saccading 12° peripherally. In this dataset there were trials in which fixation was required instead of a saccade. From this dataset onwards ITI was recorded as well| | ||
- | |2.4| Memory saccades, rectangular grid of targets starting at -12°, 0°, +12°, or -15°, 0°, +15° In this dataset there were trials in which fixation was required instead of a saccade | | ||
- | |3| Reach dataset| | ||
- | |3.1| Reach dataset, joint reach task| | ||
- | |||
- | To differentiate inactivation from control runs, we also indicate this by assigning a different data(sub-)set. Ideally, following the logic above, this would mean something like 3.5 for control and 3.6 for inactivation. Currently 31 and 32 are used respectively. For convention, Inactivation data(sub-)set value should always be higher than the respective control. | ||
- | |||
- | ==== Other entries ??? ==== | ||
- | ^Difficult_sorting_or_unstable_ ^Other_potential_reasons_to_ignore_or_check ^Runcomplete ^Usable ^Comments ^task ^ | ||
- | |||
- | |||
- | ===== plx files table ===== | ||
- | |||
- | |||
- | ===== automatic processing logs ===== | ||
ephys_pipeline/4_meta-info.1641928503.txt.gz · Last modified: 2022/12/29 07:15 (external edit)