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

Currently, pyisx is only supported for x86 architectures, which can be problematic, specifically on the newer Mac computers with Apple Silicon. For usage with Apple Silicon, the Rosetta software must be installed, and the Terminal app must be configured to use this software for automatic translation of x86 binaries to arm64. Read more here on how to configure Rosetta on Mac computers.

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.