ephys_pipeline:3_sorting
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ephys_pipeline:3_sorting [2022/01/11 20:16] – [Waveclus preprocessing workflow] lukas.schneider | ephys_pipeline:3_sorting [2022/03/17 14:09] (current) – removed lukas.schneider | ||
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- | ====== Sorting ====== | ||
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- | Currently, there are 3 different sorting approaches implemented | ||
- | * Waveclus sorting (with potential to refine sorting in plexon) | ||
- | * Snippets sorting (sorting online detected spikes with plexon) | ||
- | * Realigned snippets sorting (re-aligning online detected spikes with plexon) | ||
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- | The latter two are basically identical in terms of workflow, so they are described in the same section. | ||
- | For the waveclus pipeline, waveclus preprocessing to create snippets from Broadband is required. | ||
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- | ===== Sorting pipeline ===== | ||
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- | - Fill in [[ephys_pipeline: | ||
- | - WC: Create waveclus pre-clustering files (implemented in [[ephys_pipeline: | ||
- | - WC: Run waveclus and sort for all channels, don’t forget to save (wave_clus3new3, | ||
- | * Preferentially separate spike shapes in difficult cases | ||
- | - Create plxfiles (implemented in [[ephys_pipeline: | ||
- | - Check and clean PLX file and **TAKE NOTES** (single/ | ||
- | - Now we need to assess which units are the same within and across blocks (based on channel, electrode depths, spike shapes and potentially tuning, carefully check notes for this). For that purpose you might want to do the following steps in any order (potentially even going back and forth): | ||
- | * Create combined (phys+behavior) files (implemented in [[ephys_pipeline: | ||
- | * Assign same cells across blocks in [[ephys_pipeline: | ||
- | * Plot single unit tuning assuming cells are unique in every block (implemented in [[ephys_pipeline: | ||
- | * Re-sort PLX file (combining same cells sort codes of same block same channel) | ||
- | - If you have finalized the sorting, create combined (phys+behavior) files (implemented in [[ephys_pipeline: | ||
- | - Complete [[ephys_pipeline: | ||
- | - Automatically update the automatic_sorting sheet from the [[ephys_pipeline: | ||
- | - Copy the automatic_soting entries to the final_sorting sheet of the [[ephys_pipeline: | ||
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- | ===== Waveclus preprocessing workflow ===== | ||
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- | {{: | ||
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- | ===== Waveclus (pre-)sorting ===== | ||
- | How to use waveclus to sort spikes is a topic on its own, please see Waveclus for more detailed information | ||
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- | ===== Plexon workflow ===== | ||
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- | {{: | ||
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- | ===== Plexon sorting ===== | ||
- | Sorting in plexon is - similar to waveclus - a topic on its own. | ||
- | However, there are a few internal rules: | ||
- | * usually the biggest units are put first - this makes assigning same cells easier | ||
- | * You can cut off in time if there is a specific section where sorting does not work | ||
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- | ==== Problems with online detected snippets ==== | ||
- | {{: | ||
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- | All of these issues can make online snippet sorting very difficult. However, realigned snippets will have the (due to shift) missing information padded with 0's. This means that shifted snippets might appear like a different cluster. So they will potentially have to be sorted with redefined principle components for each subset. | ||
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- | ==== Plexon file naming ==== | ||
- | Session_blocks_N.plx are based on online snippets | ||
- | \\ Session_realigned_blocks_N.plx are based on realigned online snippets | ||
- | \\ Session_from_BB_blocks_N.plx are based on waveclus clustering | ||
- | \\ Importantly, | ||
ephys_pipeline/3_sorting.1641932205.txt.gz · Last modified: 2022/12/29 07:15 (external edit)