pupil-analysis 0.4.1

Spatial motion analysis program

Pseudopupil Analysis suite

Specialised spatial motion analysis software for Pupil Imsoft data.

In general, can be used for data that follows hierarchy

data_directory
├── specimen_01
│   ├── experiment_01
│   │   ├── image_001.tif
│   │   └── image_002.tif
│   └── ...
└── ...

Installing

There are two supported installation ways at the moment. On Windows, the stand-alone installer is possibly the best option unless you feel familiar with Python. On other platforms, use pip.

Installer on Windows (easiest)

A Windows installer that bundles together the Pseudopupil Analysis suite and all its depencies, including a complete Python runtime, is provided at Releases.

The installer creates a start menu shorcut called Pupil Analysis, which can be used to launch the program.

To uninstall, use Add or Remove programs feature in Windows.

Using pip (the python standard way)

The latest version from PyPi can be installed with the command

pip install pupil-analysis

This should install all the required dependencies, except when on Windows, OpenCV may require Visual C++ Runtime 2015 to be installed.

Afterwards, to upgrade an existing installation to the latest version

pip install --upgrade pupil-analysis

In case of regressions, a specific version of the suite (for example 0.1.2) can be installed

pip install pupil-analysis==0.1.2

Finally, to open the program

python -m pupilanalysis.tkgui

How to use

First, open a data directory (containing the folders containing the images). Next, select the regions of interest (ROIs) and then run the motion analysis. The ROIs and movements are saved on disk (C:\Users\USER\PupilAnalysis or /home/USER/.pupilanalysis), so these steps are needed only once per specimen.

After the initial steps you, can perform further analyses in the program or export the data by

1. copy-pasting to your favourite spread sheet or plotting program or 2) exporting CSV files.

Notes

This is still an early development version (expect rough edges).