Contribute

Example Datasets

Example datasets are maintained at https://gin.g-node.org/CatalystNeuro/ophys_testing_data.

To download test data on your machine,

1. Install the gin client (instructions here)

2. Use gin to download data:

   gin get CatalystNeuro/ophys_testing_data
   cd ophys_testing_data
   gin get-content
   

3. Change the file at roiextractors/tests/gin_test_config.json to point to the path of this test data

To update data later, cd into the test directory and run gin get-content

Troubleshooting

Installing SIMA with python>=3.7:

Will need a manual installation for package dependency SIMA since it does not currently support python 3.7:

1. Download SIMA wheels distribution here.

2. pip install <download-path-to-wheels.whl>

3. pip install roiextractors

More details on how to construct individual extractors can be found here:

Contents:

• 1. Build an ImagingExtractor:
• 2. Build a SegmentationExtractor: