Overview

isx is a python package for interacting with Inscopix data. This package encapsulates the following I/O functionality:

Reading Inscopix files (.isxd, .isxb, .gpio, .imu)
Writing Inscopix files (.isxd)
Exporting Inscopix files to third-party formats (.mp4, .tiff, .csv)

The isx package is built from the pyisx project, a python binding for isxcore, a C++ API for interacting with Inscopix data.

Install

This package is available on pypi. To install isx, run the following command in a python environment:

pip install isx

Attention

For Apple Silicon (i.e., macOS with arm64 architecture), the package is currently not natively supported. However, it’s possible to use anaconda to configure an x86 environment and use the project.

CONDA_SUBDIR=osx-64 conda create -n <name> python=<python>
conda activate <name>
conda config --env --set subdir osx-64
pip install isx

Please refer to the Installation guide for more details.

File Types

This package encapsulates the following I/O functionality:

The following table summarizes all Inscopix file types and the functionality supported by this package:

File Type	File Format	Read	Write	Export	Description
`Microscope Movie`	`.isxd`	Yes	Yes	`.mp4`, `.tiff`, `.csv`	Recording acquired from a microscope
`Microscope Image`	`.isxd`	Yes	Yes	`.tiff`	Image acquired from a microscope
`Behavior Movie`	`.isxb`	Yes	No	`.mp4`	Compressed recording acquired from a behavior camera
`Cell Set`	`.isxd`	Yes	Yes	`.tiff`, `.csv`	Neural cells represented as a set of temporal activity traces and spatial footprints. A `Cell Set` is generated from a `Microscope Movie`
`Event Set`	`.isxd`	Yes	Yes	`.csv`	Neural events (e.g., calcium events) represented as a set of discrete signal traces. An `Event Set` is generated from a `Cell Set`
`Vessel Set`	`.isxd`	Yes	Yes	`.tiff`, `.csv`	Vessels represented as a set of vessel diameter or red blood cell (rbc) velocity traces. A `Vessel Set` is generated from a blood flow `Microscope Movie`
`GPIO`	`.gpio`, `.isxd`	Yes	No	`.isxd`, `.csv`	General purpose input/output signals recorded from an acquisition device
`IMU`	`.imu`	Yes	No	`.isxd`, `.csv`	Inertial measurement unit (accelerometer, magnetometer, orientation) recorded from an acquisition device
`Compressed Microscope Movie`	`.isxc`	No	No	N/A	Compressed recording acquired from a microscope. A `Compressed Microscope Movie` is decompressed into a `Microscope Movie`

Next Steps

To learn more about how to use the isx package, refer to the Examples guide and the API Reference.