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deephys's Introduction

Welcome to DeePhys

The package for Deep electrophysiological phenotype characterization:

Analysis schematic

Created with BioRender

Overview

DeePhys was created to facilitate the analysis of extracellular recordings of neuronal cultures using high-density microelectrode arrays (HD-MEAs). DeePhys allows users to easily:

  • Extract electrophysiological features from spikesorted HD-MEA recordings
  • Visualize differential developmental trajectories
  • Apply machine learning algorithms to classify different conditions
  • Obtain biomarkers predictive of the respective condition
  • Evaluate the effect of treatments
  • Dissect heterogeneous cell populations/cultures on the single-cell level

Requirements

Currently DeePhys is only available on MATLAB, so a recent MATLAB installation (>2019b) is required. We plan on expanding DeePhys to Python in the near future.

Installation

The package is ready-to-use right after cloning. As the download via git-lfs is heavily limited, please download the spike sorted data for the tutorial here and replace the folder SortingExamples with the unzipped version from there. Preprocessed data can be downloaded here.

Usage

Code requires spikesorted data in the phy format. For help with spikesorting check out the Spikeinterface package.

The analysis pipeline is subdivided into the following modules (links to the tutorials):

Citation

The DeePhys package was first published on bioRxiv, but was since heavily updated and is no longer compatible to the prior version.

Disclaimer

This package uses several packages/toolboxes:

deephys's People

Contributors

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deephys's Issues

Error in FeatureExtraction for maxtwo data and few other questions.

You can assign this a label, "question", also it would be great to have a discussion page on the repo

Iam trying to understand the modules , but while trying to run featureextaraction on a sorted data from a maxtwo recording I faced this error, any insights on this:

BasicFeatureExtractionTutorial
Generated 1 sorting paths
Loaded recording information
Imported custom parameters
Found 1 units with bad power
Found 0 units with bad amplitudes
Found 13 units with bad firing rates
Found 15 units with bad RPV
Identified 31 units as axonal
Identified 65 units as noise
Found 680/785 good units
Index in position 1 is invalid. Array indices must be positive integers or logical values.

Error in MEArecording/inferWaveformFeatures (line 280)
            peak_1_cutout = interp_wf_matrix(unit_trough_idx - ms_conversion:unit_trough_idx,:); %Limit detection range for peaks

Error in MEArecording/generateUnits (line 613)
               waveform_features = obj.inferWaveformFeatures(good_amplitudes, good_wf_matrix);

Error in MEArecording/performAnalyses (line 130)
                obj.generateUnits();

Error in MEArecording (line 37)
                mearec.performAnalyses();

Error in generate_MEArecordings_from_sorting_list (line 50)
                    rec_array{iPath} = MEArecording(metadata, params);

Error in BasicFeatureExtractionTutorial (line 57)
rec_array = generate_MEArecordings_from_sorting_list(sorting_path_list, lookup_path, path_part_idx, params.QC.N_Units, params, parallel);
 

I initially suspected it was due to the maxtwo sampling but few other examples worked fine. any insights on these be great.

also I have a few more questions,

  1. do you sort on the activity assays ( as in Silvia Ronchis paper)?

  2. Why use KS 2.5, i was using KS2 since the cells are stationary.

  3. When I went through your paper, I understood for a culture representative unit and waveforrm features were calculated, since we use mouse primary neurons, there is a mix of different cells, i want to segregate them into excitatory and inhibitory. Can I use your module to this, any thoughts on this. Thank you for your time.

readNPYheader Error while using sortingExample data for running the Feature extraction tutorial.

While using the given spike_templates.npy , the following error is thrown.

`Error using readNPYheader
Error: This file does not appear to be NUMPY format based on the header.

Error in readNPY (line 10)
[shape, dataType, fortranOrder, littleEndian, totalHeaderLength, ~] = readNPYheader(filename);

Error in generate_MEArecordings_from_sorting_list (line 49)
spk_temp = readNPY(temp_file);

Error in MandarBasicFeatureExtractionTutorial (line 60)
rec_array = generate_MEArecordings_from_sorting_list(sorting_path_list, lookup_path, path_part_idx, params.QC.N_Units, params, parallel);
`

I kindly request you to provide a proper sample data to run the tutorials. Thank you

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