# 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](https://github.com/inscopix/isxcore), a C++ API for interacting with Inscopix data.

## Install


This package is available on [pypi](https://pypi.org/project/isx/).
To install `isx`, run the following command in a python environment:

```python
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](https://support.apple.com/en-us/102527) on how to configure Rosetta on Mac computers.
:::

Please refer to the [Installation](#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](#examples) guide and the [API Reference](#reference).