Skip to content

GH-#518 Add NWB epoch support for epochs saved from MIES in NWB - #593

Open
MichaelHuth wants to merge 2 commits into
masterfrom
GH-518/feature/add-support-for-mies-epochs
Open

GH-#518 Add NWB epoch support for epochs saved from MIES in NWB#593
MichaelHuth wants to merge 2 commits into
masterfrom
GH-518/feature/add-support-for-mies-epochs

Conversation

@MichaelHuth

@MichaelHuth MichaelHuth commented Aug 12, 2026

Copy link
Copy Markdown
Collaborator

When loading NWB files exported with MIES then the epoch information is parsed in ipfx as well.

The API stays compatible, epochs can be retrieved as before when the sweeps object is constructed. Epoch names from nwb are prefixed with "nwb:" to set them apart from the already existing epochs.

So for epoch "E0" in MIES the epoch name in ipfx is "nwb:E0".

Thank you for contributing to the IPFX, your work and time will help to
advance open science!

Close #518

Type of Fix:

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing
    functionality to not work as expected)
  • Documentation Change

Checklist

  • My code follows
    Allen Institute Contribution Guidelines
  • My code is unit tested and does not decrease test coverage
  • I have performed a self review of my own code
  • My code is well-documented, and the docstrings conform to
    Numpy Standards
  • I have updated the documentation of the repository where
    appropriate
  • The header on my commit includes the issue number
  • My code passes all tests
  • I have updated the CHANGELOG.md with the description of changes understandable by end users

- The API stays compatible, epochs can be retrieved as before when the
sweeps object is constructed. Epoch names from nwb are prefixed with
"nwb:" to set them apart from the already existing epochs.

So for epoch "E0" in MIES the epoch name in ipfx is "nwb:E0".
This example program allows to load a nwb file.
The user can select a sweep through a slider and
two independent epochs. For each slice of the sweep the
SpikeFeatureExtractor is run and the results are displayed on top
of the sweep data in a plot.

The example requires the python package PySide6
@MichaelHuth

Copy link
Copy Markdown
Collaborator Author

@timjarsky I created an example program that allows to use the SpikeFeatureExtractor with two independent selectable epochs:

image

Minimum steps to run the example, from a Windows command prompt in the
checked-out ipfx repo root:

pip install -e .
pip install PySide6
python examples\interactive_epoch_spike_viewer.py

optionally you can also give an nwb file as command line argument to open it at startup.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Projects

None yet

Development

Successfully merging this pull request may close these issues.

Read epochs info from nwb2 files

2 participants