sweep qc tool

A GUI application for performing manual quality control on in vitro ephys experiments.

installation

We provide binary packages for Windows, which you can download from the releases page. To install on Windows:

1. download sweep_qc_tool.zip
2. unzip the archive and move the resulting directory to your desired install location
3. run sweep_qc_tool.exe to start the tool

To run on OSX or Linux you should:

1. clone this repository to your desired install location using git clone https://github.com/alleninstitute/sweep_qc_tool
2. create an environment using e.g. conda or virtualenv. For instance, if using virtualenv on Linux, you might run:

   cd sweep_qc_tool
   python3 -m venv .venv
   

   to create your virtual environment. You would then activate this environment using source .venv/bin/activate.
3. With your environment activated, install the dependencies by running

   pip install -r requirements/base.txt
   

4. You can now start the tool either via fbs run or via python src/main/python/main.py.)

If you invoke the sweep qc tool from the command line, you can customize its behavior by passing optional arguments. See the main file for documentation of these parameters.

usage

QCing sweeps

With the tool running, you will most likely want to load some data! Navigate to File->load data set from NWB file and select the NWB file containing your data in the resulting dialog. You ought to see something like:

You can get started right away QCing sweeps. Whenever you see an auto QC state that looks wrong, adjust the manual QC state from default to passed or failed using the dropdown menu. If you want a closer look at one of the images, simply click the thumbnail for an zoomable and pannable popup plot: When you are done, select File->Export manual states to JSON to save your work.

Viewing extracted features

In the bottom right corner of the sweep page (the first image above) you should see a red message warning that cell features are outdated. Indeed, if you switch over to the Features tab, you will see a blank page! To calculate cell-level features, use Edit->Run feature extraction. Now when you select the Features tab, you ought to see something like this (after a short wait): When you run feature extraction, cell-level features are calculated using the set of passed sweeps. Each time you change this set by failing or passing a sweep, the cell features become outdated, and the warning message will return.

level of support

We are actively using and maintaing this code. We welcome issues (particularly bug reports) and pull requests from the community, but cannot promise to address them on any fixed schedule.