PupilEXT: flexible open-source platform for high resolution pupillometry in vision research

This repository provides the official implementation of a free pupillometry cross-platform (MacOS, Windows, Linux) system called PupilEXT proposed in the article "PupilEXT: flexible open-source platform for high resolution pupillometry in vision research" authored by Babak Zandi, Moritz Lode, Alexander Herzog, Georgios Sakas and Tran Quoc Khanh from the Technical University of Darmstadt.

PupilEXT can record eye images using a stereo camera system or a single camera to measure the pupil diameter in real-time. Additionally, it is possible to analyse externally-recorded images without connected cameras through the PupilEXT interface.

We aimed to provide a professional open-source pupillometry measurement platform, making an easy and inexpensive entry into pupil research for interdisciplinary research groups possible. PupilEXT integrates high-resolution industrial cameras from Basler. The pupil detection itself can be performed with one of the state-of-the-art open-source algorithms, Starburst [1], Swirski2D [2], ExCuSe [3], ElSe [4], PuRe [5], and PuReST [6].

[Paper] [Supplementary materials]

Features of PupilEXT (v0.1.2)

For initial testing, we recommend using the provided demo datasets. See section 2.4 in this repository. Pay attention to the image playback speed setting, if you are on a laptop with low computational power.

IMPORTANT information about the Community Branch of PupilEXT (v0.1.2)

This branch contains the Experimental Community Version of PupilEXT, maintained by Gábor Bényei (kheki4) and Attila Boncsér (sasfog). More information can be found in the readme of the project (Link: https://github.com/openPupil/Open-PupilEXT/tree/Experimental-Community-Version/Community).

Note that this version of PupilEXT is subject of ongoing development to further add new features and might contain bugs or other errors. New features have already been developed, but they are under testing.

Planned features are going to be published under the issues page, while a public discussion will be maintained to keep track of the development and discuss any new feature suggestions. Note that this program is distributed in the hope that it will be useful, but without any warranty, without even the implied warranty of fitness for a particular purpose.

Correspondence for this community version can be adressed to: Gábor Bényei (kheki4): [email protected] Attila Boncsér (sasfog): [email protected]

Questions?

If you have new ideas, questions or want to discuss some extended topics, please use our discussion forum: https://github.com/openPupil/Open-PupilEXT/discussions

!! NEW 08/2024 !!: Release v0.1.2 based on the Experimental-Community-Version branch

A new branch called Experimental-Community-Version has been created to support community additions. Its maintainers are Gábor Bényei and Attila Boncsér. For further information check out the community README.

!! NEW 04/2022 !!: A Python version of PupilEXT is now available.

Note that the Python package of PupilEXT is currently in the experimental stage.

Link to the GitHub repo of PyPupilEXT: https://github.com/openPupil/PyPupilEXT

Note: The animation above shows PupilEXT v0.1.1.

1. Overview

PupilEXT is a real-time pupillometry software whose graphical user interface is mainly programmed using C++ (QT. 5.15) and can be used to integrate high-resolution industrial cameras for online measurements. This Repository provides a guide on how to install, set up and use the system for pupillometry. Before using the PupilEXT framework, we recommend reading the work "PupilEXT: flexible open-source platform for high resolution pupillometry in vision research".

1.1 Pupillometry setup configuations

With PupilEXT, you can detect the pupil diameter with three different setup configurations (see Figure). In the stereo camera configuration, the pupil diameter can be recorded directly in millimetres through an internal triangulation procedure. In the simplest case, only one camera must be connected for measuring the pupil diameter in pixels. The conversion from pixels to mm can then manually be performed using a circular reference object. If no camera is available, PupilEXT offers the possibility to load externally recorded images for offline analysis. The externally acquired images can be treated as a live feed, unlocking the full functionality of PupilEXT.

1.2 Hardware and software requirements

Depending on which setup configuration is used, additional hardware components must be purchased. Below is a list of components with which our demo system was built. In general, the USB3 Basler branded camera should be compatible with PupilEXT, as we use Pylon. GigE cameras from Basler are also compatible (suitable for longer cable distances), but we have not yet tested them. For offline analysis with externally captured images, none of the listed hardware components is necessary. In any case, the Pylon Camera Software Suite from Basler must be installed on your system, as the drivers are needed to start PupilEXT, even if no camera(s) is connected. Check out our publication if you need additional information on how to build the hardware system.

Components: Stereo camera configuration (identical to setup in Zandi et al., 2021)*

2 x Basler acA2040-120um (USB3 cameras)
2 x KOWA LM50JC3M2 (2/3" C-Mount lenses)
2 x Schneider IF 092 SH 27.0 (Filters)
2 x H06S Power I/O Cable
1 x STM32 Nucleo F767ZI or similar (Hardware trigger)
1 x IR-illumination (Recommended)

Components: Single camera configuration (identical to setup in Zandi et al., 2021)*

1 x Basler acA2040-120um (USB3 cameras)
1 x KOWA LM50JC3M2 (2/3" C-Mount lense)
1 x Schneider IF 092 SH 27.0 (Red & NIR Color Filter)
1 x H06S Power I/O Cable (Optional)
1 x STM32 Nucleo F767ZI or similar (Optional)
1 x IR-illumination (Recommended)

*Note: If you wish to defer from the setup Zandi et al., 2021 used in their debut paper about PupilEXT (v0.1.1), you can also use different hardware. Anyway they also tested their system with acA1300-200um cameras, and note that the system should work with Basler dart series, though they did not test the latter. Virtually, you can opt for any other global shutter monochrome Basler camera matching your FPS needs, and a suitable lens matching with sensor size recommendation of the manufacturer. Starting from PupilEXT release v0.1.2 you can also use an Arduino Uno now, and also an ethernet connection between PupilEXT and the microcontroller to use hardware-triggered image acquisition. The developers of the Experimental-Community-Version branch also tested a2A1920-160um and used it with success. GigE and CoaXpress interface should also work, though not yet tested. For optical filter, any 720nm IR-pass element is suitable. Also, we do not recommend using UVC cameras ("webcams") for research-grade use, only for educative purposes.

Please use our discussion forum to share your ideas, setup and experience with PupilEXT with other community members:

https://github.com/openPupil/Open-PupilEXT/discussions

2. Getting started: The easy way

2.1. Installation on MacOS (MacOS 12.7.6 or later)

The direct installation requires that you have MacOS 12.7.6 or later installed on your machine. If this is not the case, you likely need to build PupilEXT from source, as the provided pre-build binaries in this section will only work on MacOS 12.7.6 or later. You can try on an earlier version of MacOS, but you are not quaranteed to succeed.

Step 1: Download and install the Pylon Camera Softwware

Download the Pylon Camera Software Suite (*.dmg) from the Basler Website:

https://www.baslerweb.com/de/vertrieb-support/downloads/downloads-software/

We tested PupilEXT with Pylon 6.2.0. (on Windows only Pylon 6.2.0. works, see the Win instructions below). If the Pylon installation does not start because of a security warning from Apple: Open the system preferences from MacOS, click on "security & privacy" and press "Open Anyway" under the "General" tab. During the Pylon installation, ensure that a complete installation is carried out with the C++ binaries (Important!). For this, you need to choose the "custom" profile and activate all checkboxes under "Pylon runtime" and "SDKs". The Pylon library is necessary for PupilEXT to control and communicate with Basler branded cameras. The installation is also needed if no camera is connected, as the Basler drivers are part of the software.

Please test your Baslers camera(s) with the installed Pylon Viewer from Basler (see Basler-Documentation: Pylon Viewer) before driving the camera(s) with PupilEXT.

Step 2: Download and run PupilEXT

We have built and deployed PupilEXT for MacOS 12.7.6 or later. You only need to download PupilEXT and open it. If you run into security warnings from Apple, you need to open the system preferences, click on "security & privacy" and then press "Open Anyway" under the "General" tab.

Download PupilEXT Version 0.1.2 Beta (MacOS) from the release page of the project's GitHub repository:

https://github.com/openPupil/Open-PupilEXT/releases/tag/v0.1.2-beta

After you have downloaded the software, you can open the dmg file and run PupilEXT (see animation). We built and tested the program on a Mac Mini 2014 Late (Intel) with MacOS Monterey (Version 12.7.6). If you run into issues, you need to build PupilEXT from source.

Note: The animation above shows PupilEXT v0.1.1.

Step 3: Testing with the demo datasets

You can load the provided demo dataset (see section 2.4) into PupilEXT for initial testing and enjoying the features during offline analysis.

2.2. Installation on Windows 10 (64 bit)

Step 1: Download and install the Pylon Camera Softwware

Download the Pylon Camera Software Suite (*.exe) from the Basler Website:

https://www.baslerweb.com/de/vertrieb-support/downloads/downloads-software/

We tested PupilEXT with Pylon 6.2.0. on several fresh installed Windows 10 (64 bit) machines. During the Pylon installation, ensure that a complete installation is carried out with the C++ binaries (Important!). For this, you need to choose the "custom" profile and activate all checkboxes under "Pylon runtime" and "SDKs". The Pylon library is necessary for PupilEXT to control and communicate with Basler branded cameras. The installation is also needed when no camera is connected, as the Basler drivers are part of the software.

Please test your camera with the installed Pylon Viewer from Basler (see Basler-Documentation: Pylon Viewer) before driving the cameras with PupilEXT.

Step 2: Download and run PupilEXT

For Windows, we have already built the software so that PupilEXT can simply be downloaded and will start without any further dependencies. Unpack the downloaded zip file and open PupilEXT.exe. It should run, as we tested it on several systems. However, if you run into unknown issues, you need to build PupilEXT from source (see instructions below).

Download PupilEXT Version 0.1.2 Beta (Windows) from the release page of the project's GitHub repository:

https://github.com/openPupil/Open-PupilEXT/releases/tag/v0.1.2-beta

Step 3: Testing with the demo datasets

You can load the provided demo dataset (see section 2.4) into PupilEXT for initial testing and enjoying the features during offline analysis.

2.3. Setup the microcontroller for the stereo camera configuration

A microcontroller is necessary if a real-time online pupil measurement should be carried out with a stereo camera system. The microcontroller has the task of generating a so-called electrical hardware-trigger, which is used to trigger the image acquisition on the camera (see Basler-Documentation: Triggering). The electrical hardware-trigger consists of a timed voltage signal of 3.3 V, which is applied to one of the camera's GPIO-Pins. If a sequence of images need to be acquired with a stable FPS, the hardware-trigger is a PWM-signal with a fixed frequency (see Basler-Documentation: Trigger-Types and Basler-Documentation: GPIO Lines). The advantage of acquiring images through a hardware-trigger signal is that the electrical signal can be connected parallel to both cameras, leading to a highly synchronized image recording. Synchronous image acquisition from both cameras is essential in a stereo camera system; otherwise, the conversion from pixels to mm is not reliable. The PupilEXT v0.1.2 software uses a hardware-trigger from an external microcontroller (STM32 Nucleo or Arduino) to acquire images from the stereo camera system. If you only want to use a single camera for pupil measurement, section 2.3 is not relevant for you.

In this way, the image capture process is as follows: The PupilEXT software sends a command (Protocol) to the microcontroller via USB (uart), aiming to start a logical hardware-trigger signal, which is transmitted from the microcontroller to the camera(s). The captured images are passed directly from the camera to PupilEXT via USB3. In continuous shooting, PupilEXT sends a command to let the microcontroller generate a continuous PWM signal, so there is no need for a single command for each trigger signal. This procedure is standard for all professional stereo camera systems. Hardware trigger signals can also be generated from the camera itself, but there is a risk that due to internal delays, the images will not be captured synchronously. Therefore, adding an external signal generator increases the stability of the system.

Since a standardised protocol between the PupilEXT software and the microcontroller is required, we have uploaded the corresponding embedded code in this repository in Misc/Microcontroller/STMNucleo_F767ZI and Misc/Microcontroller/STMNucleo_L432KC and Misc/Microcontroller/Arduino_Uno for versions to be connected with USB-emulated serial cable connection, and Misc/Microcontroller/Arduino_Uno_Ethernet for a version also supporting Ethernet-cable connection between PupilEXT and the microcontroller using a common W5500 ethernet shield. The STM Nucleo embedded projects were created using PlatformIO in Visual Studio Code. You can use either an STM32 Nucleo F767ZI or STM32 Nucleo L432KC microcontroller to flash our provided code to the microcontroller, and for the Arduino project files, Arduino IDE was used. Alternatively, you can use your own microcontroller and any desired IDE, but you must pay attention to the communication protocol (see our publication).

The following part of this walkthrough sets up the STM Nucleo. For Arduino Uno implementation, at the moment there is no specific walkthrough, but will likely be added in the future. (However, it is fairly easy to set up the Arduino version: you just need an Arduino Uno, and optionally a W5500 Ethernet shield, and the Arduino IDE to upload the code.)

We used the Mbed 5 framework for programming the STM32 Nucleo microcontroller. To simplify the flashing process for you, we highly recommend flashing the microcontroller using Mbed Studio, as this is more user-friendly. Below is a step-by-step guide on how to flash the microcontroller with Mbed Studio.

Step 1: Installation of Mbed Studio

Download and install Mbed Studio. A free account is required before you can use it.

https://os.mbed.com/studio/

Step 2: Flash the microcontroller

Create a new project inside Mbed Studio and select your connected microcontroller from the list. In the following, we assume that you are using an STM32 Nucleo L432KC. Be sure to select Mbed OS 5 as a template from the list. You can select an empty programme as template. In the fresh created main.cpp file, paste the below-listed code and press the play button in Mbed Studio (Build profile: Release) to flash the microcontroller. If you are using an STM32 Nucleo F767ZI, use another code from the file Misc/Microcontroller/STMNucleo_F767ZI/src/main.cpp, as the pin assignment is different.

#include "RawSerial.h"
#include "mbed.h"
#include <string>
#include <stdio.h>
#include <stdlib.h>

#define BUFF_LENGTH 15
#define BAUDRATE 115200

#define TX_PIN USBTX
#define RX_PIN USBRX

#define LED_PIN_1 LED1
#define Trigger_Pin PB_0

RawSerial pc(TX_PIN, RX_PIN);
volatile char rx_buf[BUFF_LENGTH];
Timer timer_Stopper;

DigitalOut LED_Green(LED_PIN_1);
DigitalOut Trigger(Trigger_Pin);
Ticker myTick;

// Global Values
char M_or_T; // T = Manually Trigger Mode
uint32_t Manually_Values[2];
uint32_t Automatic_Values[1];

volatile int flag_1 = 0;
volatile int flag_2 = 0;
int LED_ticker = 0;
int Threshold_Ticker = 0;
int STOP = 0;

void onTick() {
  LED_Green = !LED_Green;
  Trigger = !Trigger;
  LED_ticker++;
  if (LED_ticker >= 2 * Threshold_Ticker && Threshold_Ticker!=0) { // This line was modified to check "&& Threshold_Ticker!=0" by Gabor Benyei
    myTick.detach();
    LED_Green = 0;
    Trigger = 0;
  }
  if (STOP == 1) {
    myTick.detach();
    LED_Green = 0;
    Trigger = 0;
  }
}

void serialCb() {

  char *pch;
  pch = strtok((char *)rx_buf, "X");

  M_or_T = *pch;

  if (M_or_T == 'T') {
    pch = strtok(NULL, "X");
    Manually_Values[0] = atoi(pch);

    pch = strtok(NULL, "X");
    Manually_Values[1] = atoi(pch);
  }

  switch (M_or_T) {

  case 'T':
    Threshold_Ticker = Manually_Values[0];
    STOP = 0;
    LED_ticker = 0;
    myTick.attach_us(&onTick, Manually_Values[1]);
    break;

  case 'S':
    STOP = 1;
    break;

  default:
    break;
  }
}

void callback() {
  if (pc.getc() == '<') {
    pc.putc('<');
    for (int i = 0; i < 20; i++) {

      rx_buf[i] = pc.getc();

      if (rx_buf[i] != '>') {
        pc.putc(rx_buf[i]);
      }

      if (rx_buf[i] == '>') {
        pc.putc('>');
        pc.putc('\n');
        flag_1 = 1;
        break;
      }
    }
  }
}

int main() {
  LED_Green = 0;
  LED_ticker = 0;
  Trigger = 0;
  pc.baud(115200);
  pc.attach(&callback, Serial::RxIrq);
  pc.printf("Program started! \n");

  while (1) {
    if (flag_1 == 1) {
      serialCb();
      flag_1 = 0;
    }
  }
}
// STM32 Nucleo L432KC flashing code
// The provided code for the STM32 Nucleo is licensed under the MIT
// See the lincense file in this repostory:
// Microcontroller/STMNucleo_L432KC/LICENSE

Step 3: Wire the components together:

Plug the two purchased I/O cables (see section 1.2: Hardware requirements) into the I/O connector of camera 1 and 2. At the open end of the I/O cable are the respective 6 I/O lines of the camera. PIN 1, corresponding to Line 3 of the I/O cable can be used to apply a logical hardware trigger signal to the Basler acA2040-120um camera. Please read the documentation and warnings of your camera regarding the I/O PINs, otherwise you may damage your camera if the wrong voltage values are used (see Basler-Manual: GPIO Lines). Pay attention to the correct PIN numbers of the I/O connector and check the camera's documentation to see which I/O PIN is the correct one for your case: https://docs.baslerweb.com/aca2040-120um

Connect the respective I/O line of camera 1 and camera 2 in parallel with the trigger PIN on the microcontroller. If you have used our embedded code to flash the microcontroller, it is PIN PB_0 on the STM32 Nucleo L432KC or PIN PC_6 on the STM32 Nucleo F767ZI. You can check where the PIN is located on the board by checking the Mbed webpage:

Pinout sketch STM32 Nucleo L432KC: https://os.mbed.com/platforms/ST-Nucleo-L432KC/

Pinout sketch STM32 Nucleo F767ZI: https://os.mbed.com/platforms/ST-Nucleo-F767ZI/

We recommend verifying that the microcontroller has been successfully flashed. To do this, you can enter the following command (Protocol: ) in a serial monitor (Baudrate: 115200). For this, either the integrated serial monitor of Mbed Studio can be used or another one like HWMonitor or CoolTerm. This command should start a flashing green LED (10 times) on the microcontroller, with a turn-on time of 1000000 microseconds in each cycle. Since the hardware-trigger PIN of the microcontroller is "connected" to the LED, it signifies that the PC-to-microcontroller communication and the signal generation are working. Additionally, the trigger signal can be measured using an oscilloscope.

Once the microcontroller's correct operation has been checked, the cameras can be connected to the microcontroller and the PC via USB. Simultaneously, the hardware trigger PIN of the microcontroller should be connected in parallel with GPIO PINs of camera 1 and camera 2. Do not forget to connect the GND line of the camera to the GND PIN of the microcontroller. The figure in Misc/img/PupilEXT_Measuremtn_Setups.png illustrates the setup of a stereo camera configuration. After the connection has been made correctly, the PupilEXT software can be started to begin measuring the pupil diameter through the stereo camera system.

2.4. Demo dataset for offline analysis

We provide three different recorded datasets containing eye images that can be analysed using PupilEXT. This should give users the possibility to work directly with the software PupilEXT. The first two data sets were recorded using a single camera. Data set number 3 was recorded with a stereo camera system and is used in the video tutorial of PupilEXT (see section 2.5). The images were acquired directly with PupilEXT, as we offer the feature to record images for later offline measurement of the pupil diameter without connected cameras. The data set is suitable for playing around with PupilEXT and getting a first impression.

IMPORTANT NOTE: These datasets were first created for PupilEXT release v0.1.1. and they do not yet contain the image-annotations for trial-numbering and recording-related messages, you can see these functionalities working only when you make event-related pupillometry recordings using our supplied PsychoPy and Matlab PsychToolbox example codes. In the future we will upload demo datasets for the release v0.1.2 as well.

We stored the demo data in the TUdatalib repository: https://tudatalib.ulb.tu-darmstadt.de/handle/tudatalib/2929

Description	Download-Link	File-size
Recorded with a single camera under natural light with a filter in front of the lens. Dataset is without a calibration file.	Download dataset 1	1.2 Gb
Recorded with a single camera under natural light without a filter in front of the lens. Dataset is without a calibration file	Download dataset 2	600 Mb
Recorded using a stereo camera system with IR-illumination and a filter in front of the lens. Calibration files are available and loaded to PupilEXT (see instructions below).	Part 1 Part 2 Part 3	~10 Gb

Instructions on how to use the stereo camera demo data: The data set is divided into three parts. Please download all three files first. Part 1 (Stereo_camera_recording_Part_1) is the main folder containing the two subfolders Calibration_Files and Stereo_Images. The Stereo_Images subfolder is currently empty and needs to be filled with the demo images of cam 0 and cam 1. For this, download Part 2 (Stereo_camera_recording_Part_2_CAM0) and Part 3 (Stereo_camera_recording_Part_3_CAM1). Unzip the two folders and rename the folder Stereo_camera_recording_Part_2_CAM0 to 0 and also rename folder Stereo_camera_recording_Part_3_CAM1 to 1. Move the renamed folder 0 and 1 into the subfolder Stereo_Images of the main folder Stereo_camera_recording_Part_1 (Part 1). In PupilEXT, you only need to choose the subfolder Stereo_Imagesas image source. The folder 0 and 1 will be automatically assigned to cam 0 and cam 1. The individual calibration files are in the subfolder Calibration_Files. You only need to choose the stereo calibration file and not the single calibration files for each camera (see video tutorials).

Synthesized test image sets for developer contributors

Starting from the v0.1.2 source code version on the Experimental-Community-Version branch, we also include Matlab scripts that can be used to synthesize artificial pupil image sets for testing pupil detection algorithms, and the Automatic Parametrization feature of PupilEXT. These can generate artificial pupillary response signals using the most common periodic signal waveforms (triangle, sinus, sawtooth, square), and generate a perfect temporal fidelity image set corresponding to the pupillary response signals. The scripts also generate image annotation data that can be read using PupilEXT release v0.1.2 and contain trial start annotations (psychopsysiological trigger timestamps) at each waveform repetition. The script was tested using Matlab R2020b, and can be found in the folder: Misc/Matlab_Test_Image_Set_Synthesizer/

If you would like to use synthesized test image sets right now, you can just download pre-generated image sets made with the very same scripts with basic settings, here: https://drive.google.com/file/d/1l9mYBhGvpeID_vNuX0WdsBHlz-fNvrTD/view?usp=sharing

Note on externally acquired images

When loading images to PupilEXT for offline analysis, take care of proper file names. For example, if you label your files with sequenced numbers such as 1.png, 2.png, 3.png, 4.png, 5.png, 6.png, 7.png, 8.png, 9.png, 10.png, 11.png, you will run into issues, as the order of the images will be changed to 1.png, 10.png, 11.png, 2.png, ...

You need to label the images with trailing zeros (e.g. 001.png), where the number name of the image file represents the time stamp of image acquisition in milliseconds. If you recorded the images with PupilEXT, everything is labelled correctly as we use the timestamp in milliseconds as filenames. The provided demo datasets are recorded with PupilEXT.

2.5 Notes about pupil detection accuracy

The pupil detection can be determined in PupilEXT with one of the six open-source pupil detection methods Starburst [1], Swirski2D [2], ExCuSe [3], ElSe [4], PuRe [5], and PuReST [6]. The respective algorithm can be selected directly within the pupillometry interface. A pupil measurement's accuracy depends on the applied detection algorithm if the image quality and composition are ideal. Each pupil detection algorithm has a certain number of parameters (constants) that the user must set. For instance, at least the minimum or maximum possible pupil diameter must be adjusted, which can depend on the image's resolution, though beginning from PupilEXT release v0.1.2 you can also use the Automatic Parametrization feature to help with this. In PupilEXT, we offer the possibility to adjust the parameters of an applied detection algorithm, leading to more freedom in increasing the measurement accuracy. The original publications' standard parameters are usually not ideal for all measurement settings and should be adjusted if the detection rate is not good enough.

The accuracy can also be increased by selecting a specific region of interest (ROI) in the image. In this way, the algorithm no longer needs to perform pupil detection over the entire image. A smaller ROI size also reduces the calculation time, allowing a higher framerate in real-time measurements. We provide different preset settings for the algorithms` parameters which are dependent on the used ROI size. However, we highly recommend using the PuRe or PuReST algorithm, as it needs only three parameters. Furthermore, these two pupil detection algorithms are considered both the fastest and accurate in the literature and are part of the amazing open-source eye-tracking software EyeRecToo [7]. According to our preliminary investigations, the Swirski algorithm can provide better results, as it does not downscale the image before a pupil detection. The downside is that it needs a higher calculation time and has a higher number of parameters. There is the risk that the parameters do not match the image composition, leading to poor pupil detection accuracy.

2.5. How to use PupilEXT ?

New tutorial videos introducing PupilEXT release v0.1.2 are on the way. We will upload them here in the future. For using the older version (v0.1.1.) you can find videos in the archived version of this readme file.

Opening a single camera or stereo setup

To open a camera device, use the camera icon in the left (camera list is updated automatically). You can use a single camera setup without an STM Nucleo or Arduino microcontroller for hardware-triggered image acquisition (though you can, is you choose to). For stereo camera setup, you need to use a microcontroller to carry out triggering. You need to follow the numbered steps in the camera settings dialogs, in order to successfully connect to a camera and start image acquisition.

In case of stereo setups, where you have to use hardware-triggered acquisition, it follows as:

1: Connecting to the microcontroller (Can be done via Serial or Ethernet, based on your hardware setup)
2: Opening the camera pair (Can be connected via USB3 or GigE, based on your hardware setup)
3: Setting image acquisition properties that will affect you maximum possible FPS rate (smaller image acquisition ROI, larger binning, and shorter exposition time can be used to increase FPS)
4: Set the desired FPS rate (lower or equal than the maximum achievable) and start image acquisition triggering.

Opening an existing image recording

To open an image recording from the disk, you need to close any opened camera, and use the File menu/Open images directory option. You need to navigate into the directory you want to open, and press Open to open it, or just drag-and-drop an image recording folder (or any of its files inside) into the main window. PupilEXT supports several image formats for reading, so you can even use recordings that were made by another program or script, however you need to make sure that all the image files are named with trailing zeros, and their name equals the timestamp of image acquisition per each frame, in milliseconds.

You can now play back the recording using the graphical interface, which supports frame-by-frame inspection and automated playback as well. You can also jump to selected frames manually, and see trial numbering and textual messages annotated for each frame.

A live eye image will be visible in the camera view window, where you can monitor the state of pupil detection, set pupil detection ROI (software ROI, which does not affect achievable maximum FPS) and set Automatic Parametrization expected minimum and maximum pupil size (described later).

To help camera positioning you can turn on Camera Positioning Guide overlay in the Camera View window, in the Show menu, along with other useful overlays. The Positioning Guide is particularly helpful if you are using stereo cameras, that need to be pointed at the same eye or at a common target. This Positioning Guide has its center in the actual center of the camera sensor, where the lens distortion is the lowest.

Making an image recording

To start image recording, you need to set an image output directory in the left icon bar of the main window. We advise to save images to a local SATA disk with high write speed. Saved image recording size will depend on the image size you set in the camera settings dialog. If you choose large image size, recordings can eat up a very big space, so be cautious.

Also pay attention to the warmup indicator in the status bar. If it is grey, there is no sufficient data yet (1 minute) to judge whether the camera(s) have warmed up, it is red if the camera(s) is/are changing temperature, and it is green if the camera(s) reached a thermal equilibrium with their environment and is/are ready for proper recording. (Note that the actual warm-up time also depends on the illuminator you use. Right now, PupilEXT only supports checking the temperature of the camera(s), though in the future we plan to add illuminator temperature checking too. Usually an LED illuminator and its driver needs half an hour to warm up from room temperature to their operating temperature.)

In case a recording exists with the same name, you are asked whether wou would like PupilEXT to append to the existing recording, or make a new one that is automatically renamed, in a new folder. You can also set the default behaviour for these cases in Settings.

Calibrating for camera image undistortion and px-mm mapping

Calibration is an optional step that can be made to compensate for the camera lens distortion, and for proper pixel-to-millimeter mapping the measured pupil size. It is only needed when you are running PupilEXT to carry out pupil detection, writing data to e.g. a .csv file or streaming the data. For only image recording, calibration is not a must, though it should be made and saved in order to load it as an offline calibration later, when the image recording is to be processed in a calibrated manner.

Note that if you alter Image Acquisition ROI or the binning value in the Camera Settings dialog, you have to make a new calibration.

To calibrate, use a correctly-sized calibration pattern, printed on a sheet of paper, and present it to the camera(s) on a strictly flat surface (e.g. sticker on a smooth cardboard), placed in the expected eye target distance to the camera(s). The appropriate calibration routine is accessible after opening the camera(s), with the Calibrate button in the icon bar of the main window.

Setting up pupil detection

Selecting a pupil detection algorithm is a necessary step, though a default is already set upon start. PuRe and PuReST usually perform well, and are efficient, while also provide a confidence output. PupilEXT supports several pupil detection algorithms, which can be parametrized in different ways. If you just would like to use them without much customization, we advise to select the Automatic Parametrization option in the Pupil Detection Settings dialog. This configuration setting can be set for every algorithm.

We also advise to use pupil detection ROI preprocessing, using the appropriate checkbox in the same dialog. If pupil detection ROI preprocessing is enabled, only a fraction of the recorded image is scanned for pupil(s), and we highly recommend you to use this option for better performance. You can set pupil detection ROI in the Camera View window, when a camera (or image recording) is opened in the Pupil Detection menu. Please note that Image Acquisition ROI is a completely different setting, having to do with which part of the camera sensor you are reading image content from (a smaller im. acq. ROI can improve FPS).

If you have previously calibrated your camera, and it is loaded, you can opt for undistorting the pupil size on each frame inside the selected pupil detection ROI. You can also opt for undistorting the whole image, though not recommended. The easiest is to use Automatic Parametrization (recommended, and can be enabled in Pupil Detection Settings dialog). With that, you can specify the expected pupil diameter for the algorithm, using Pupil Detection menu in the Camera View window.

Using pupil tracking

To activate pupil tracking, you need to click on the Pupil tracking icon in the toolbar on the left side of main window. This function has two main use cases:

1, If you want to perform live pupil detection to write output to e.g. a .csv file or stream it on the spot
2, If you want to run analysis on previously made image recordings.

Yet, as of PupilEXT version v0.1.2 the latter is recommended, to ensure precise trial and message triggering. Now we advise to first acquire images and run pupil detection on the recordings later, to produce data files.

Making data recordings

To start .csv data file recording, you first need to set an output file path and name, using the icon toolbar on the left of the main window. It is also automatically set to a default output file name upon opening an image recording, to a .csv file located in the parent folder of the image recording folder.

In case you have been previously looking around in the recording already, now you should wind back to the first frame using the image playback control dialog. Then you may click on the red Record button to start recording, and click on the Play button of the image playback control dialog to start producing the active pupil detection output to a .csv file.

Note that yet we only recommend to record to .csv files offline, when the image set is recorded beforehand, and is analyzed for pupil detection at a later point in time. This is because the exact timing of trial increment trigger timestamps and messages received from the Experiment computer are ensured to be precise only in case of image recordings and later offline analysis.

To stop the data recording, wait until the playback reaches end (be sure to untick "Loop playback" to let it finish), and click the Stop recording icon in the toolbar on the left side of main window.

Streaming data

To stream pupil detection output, you need to first set up the streaming target, and the interface through which you would like to stream the data. The program currently supports streaming via a Serial (COM) connection and/or an Ethernet connection using UDP.

The data can be encapsulated into CSV-rows, as well as XML, JSON or YAML structures. You can stream to the same target where a Remote Control Connection is already set up from, and streaming can happen on Serial and over UDP at the same time, but only to one-one target(s).

It is highly recommended to only use streaming in case low-FPS image acquisition. You can stream pupil detection output from live camera input, but also from image recording playback, for e.g. testing purposes.

A note on reproducibility

As any scientific measurement system, PupilEXT software is built with special attention paid to research reproducibility needs. Also, as it is an open-source system, and can be used with varied hardware, it is the responsibility of the researcher mostly to minimise any between-subjects differences in data acquisition circumstances, while the software does its best to also minimise undesired within-subject variations, and offers functionalities to help the researcher with the former.

The software currently automatically saves many of its settings in a structured format alongside with image and ".csv." data recordings in an arbitrary, human-readable format: in an ".xml" file, named with a "_meta" postfix. Also, it supports storing and re-loading ALL the application settings for different subjects, using the Subjects dialog, accessible with the Subjects icon in the icon bar: in an ".ini" file, which upon loading,would reset all settings, including remote control connection, streaming, etc. The purpose of the meta files is to provide a way to manually, visually inspect any application setting related to image acquisition and pupil detection, when needed by the user at a later point in time, while the purpose of subject configurations is to provide a way to set the application to a previous state when an image or data acquisition was carried out.At the moment, these two functionalities are partly overlapping, and will be merged into one in a next release of the PupilEXT software.

2.6. Integrating PupilEXT into a cognitive science experiment

It is very easy! Starting from Pupilext release v0.1.2 you can now easily integrate PupilEXT with a PsychoPy experiment program (Builder or Coder as well) or with Matlab using Psychtoolbox. You can either use serial data cable or ethernet cable for connecting the Experiment computer (running the PsychoPy or Matlab code) and the Host computer (running PupilEXT, connected to the camera(s)).

Ready-to-use examples are included under: Misc/Experiment_Integration_Examples/.

IMPORTANT NOTE: These examples only employ image data recording for offline analysis. You can still uncomment the necessary lines and use PupilEXT with real-time pupillometry, and saving the results in a .csv file on the spot. However, we highly recommend to yet only use PupilEXT for recording the image set first, and then offline analysing it and generating the .csv then and there. Using the image recording method we successfully tested PupilEXT to be very accurate regarding trial increment trigger timestamps, though this accuracy is not ensured in case of real-time pupil detection use. If you are using PupilEXT for research-grade data acquisition, please yet use it this way.

For developers: If you are interested about what is happening under the hood (how exactly our Python and Matlab integration codes communicate with PupilEXT), you can read more about the underlying protocol in: Misc/Remote_control_commands.md. You can also remote control PupilEXT from the same physical computer for development or for special use cases, via localhost.

2.7. Starting PupilEXT with executable arguments

Starting from PupilEXT release v0.1.2, for easier usage with runtime configurations set upon executable start, you can use executable arguments. These are textual "commands" that you can specify in your icon on your desktop starting PupilEXT or in your shell script (or batch .bat file on Windows) written after the name of the executable, and upon startup, PupilEXT will use these arguments to perform actions and configure itself for which otherwise you would have to interact manually in the program. This way, PupilEXT can be started upon system power up, using an automatically run shell command, to e.g. automatically schedule system warmup half an hour before the start of an experimental session, for even more precise pupillary measurements, free from warmup system drift artefacts. Using executable arguments, you can connect to cameras right upon opening the application, and set unique settings at once, start listening to an Experiment computer connected to the Host computer, and perform many more useful actions. To read about possibilities, please see: Misc/Executable_arguments.md.

3. Build PupilEXT from source: The advanced way

If you would like to contribute to this project, extend PupilEXT with custom functions, or the provided binaries do not work on your machine, building PupilEXT on your machine is necessary. The annoying part of compiling C++ projects is the integration of third-party libraries into a project. For this, you have three options: (i) use a system package manager like brew to download and build third-party libraries; (ii) download the libraries without a package manager and build it; (iii) integrating the libraries directly into the project.

If you want to stick with option (ii) you are a professional C++ developer and do not need this tutorial. Option (i) is preferable if you have several C++ projects on your machine and want to share the libraries between the projects, saving disc space (see section 3.1 and section 3.2). However, we highly recommend option (iii), which has the advatange that the integration of thirdparty libraries is fully automated(see section 3.0). You should have intermediate knowledge of C++ programming and CMake before you follow this tutorial, as we provide no warranty.

PupilEXT needs the following libraries: Boost 1.75-0_2, Ceres 2.0.0, Eigen 3.3.9, OpenCV 4.5.1_3, QT 5.15.0, spii, tbb, pylon 6.

Important Note 1: When using [email protected] or higher, you will run into compiling issues, as boost::math::sign will not work, which is used by one of the pupil detection methods.

Important Note 2: If you want to follow option (i) or (ii) you need to remove the 'vcpkg.json' file and the '.vscode' folder.

Important Note 3: If you have run into troubles while setting up the environment, please first check out our new F.A.Q. in: Misc/Build_env_FAQ.md.

3.0 Build PupilEXT with vcpkg manifest (recommended)

The PupilEXT project contains a vcpkg.json file in which all the required C++ libraries are defined. To download and build the libraries, we use the package management software vcpkg (https://vcpkg.io/en/index.html). We have placed the vcpkg GitHub repository as a submodule under 3rdparty/vcpkg, meaning that the required libraries will be downloaded automatically to the PupilEXT project folder, regardless of your system. This has the advantage that the PupilEXT folder can be easily deleted when the C++ libraries are no longer needed. However, as the libraries are downloaded and built, care must be taken to ensure that at least 6 GB are available on the disc for the PupilEXT folder (on windows ~13 GB). However, the QT library and the Pylon drivers for the cameras will not be managed via vcpkg, so they have to be downloaded and installed manually (see step 1 and 2).

Step 1: Download and install the latest Pylon Camera Softwware

Download the Pylon Camera Software Suite (*.dmg-File) from the Basler Website: https://www.baslerweb.com/de/vertrieb-support/downloads/downloads-software/

Important: You need to modify the Open-PupilEXT/cmake/FindPylon.cmake file according to the Pylon version before you start to build the project. Please read the latest post in this discussion for more information: openPupil#21

Step 2: Download and install QT

Download the QT from the website. Please install QT 5.15: https://www.qt.io/download-open-source?hsCtaTracking=9f6a2170-a938-42df-a8e2-a9f0b1d6cdce%7C6cb0de4f-9bb5-4778-ab02-bfb62735f3e5

QT 6 or higher is currently not supported.

Step 3: Clone this repository

Type into your terminal the following command

git clone --recurse-submodules https://github.com/openPupil/Open-PupilEXT.git

The --recurse-submodules option is important, as vcpkg is a submodule. Without this option, the 3rdparty folder will not contain vcpkg packet manager.

Open the CMakeLists.tx file in the PupilEXT root and change the following line, according to your installed QT

set(QT_VERSION 5.15.2) # Change the version according to your installation

Step 4: Decide which Editor to use

Depending on which editor is used, the procedure is slightly different. We have created a summary of how to proceed if you want to use Visual Studio Code, CLion or QT Creator to start PupilEXT (see the below option 1 to 4).

Option 1: Build with Visual Studio Code

First, the following extensions must be downloaded in the editor for the procedure to work:

(1) C++ extension: https://marketplace.visualstudio.com/items?itemName=ms-vscode.cpptools

(2) Cmake extension: https://marketplace.visualstudio.com/items?itemName=twxs.cmake

(3) Cmake Tools extension: https://code.visualstudio.com/docs/cpp/cmake-linux

Then open the .vscode/settings.json file in the cloned PupilEXT folder with a text editor. The entry "VCPKG_TARGET_TRIPLET": "x64-osx" must be changed to "VCPKG_TARGET_TRIPLET": "x64-windows-static-md" if you have a Windows operating system. If you are on a Mac, leave the entry as it is. Open the project folder with Visual Studio Code and build the project. If you press build for the first time, it may take a little longer, as the required libraries are downloaded and will build automatically. Make sure that you have enough disc space on your machine.

Option 2: Build with CLion

Open the project folder with CLion. Then some settings have to be made. For this, go to CLion > Preferences > Build, Execution, Deployment in the toolbar. Choose Debug and type in the Cmake options the following command:

-DVCPKG_TARGET_TRIPLET=x64-osx -DCMAKE_TOOLCHAIN_FILE=3rdparty/vcpkg/scripts/buildsystems/vcpkg.cmake

Note that x64-osx must be changed to x64-windows-static-md, if you are on a Windows machine. Next, choose for the build directory, the following folder: build. This is very important, as the CMakeLists.txt is adjusted to find the libraries in a folder called build. By default, CLion will build the project in a folder called cmake-build-debug, which will not work with the current CMakeLists.txt. Press okay and build the project. The C++ libraries will be downloaded and build automatically for you. The first run will take some time. Make sure that you have enough disc space.

Option 3: Build with QT Creator

QTCreator also supports CMake, which means that PupilEXT can also be opened there. As with CLion, only the following options need to be added:

-DVCPKG_TARGET_TRIPLET=x64-osx -DCMAKE_TOOLCHAIN_FILE=3rdparty/vcpkg/scripts/buildsystems/vcpkg.cmake

Note that x64-osx must be changed to x64-windows-static-md, if you are on a Windows machine. Next, choose for the build directory, the following folder: build.

Option 4: Build from terminal

Open your terminal and type the following commands if you are on a Mac:

cd Open-PupilEXT

mkdir build

cd build

cmake .. -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release -DVCPKG_TARGET_TRIPLET=x64-osx -DCMAKE_TOOLCHAIN_FILE=3rdparty/vcpkg/scripts/buildsystems/vcpkg.cmake

cmake --build . --config Release

./src/PupilEXT

If you are on Windows 10 use these commands (not tested, but should be similar):

cd Open-PupilEXT

mkdir build

cd build

cmake .. -DCMAKE_BUILD_TYPE=Release -DVCPKG_TARGET_TRIPLET=x64-windows-static-md -DCMAKE_TOOLCHAIN_FILE=3rdparty/vcpkg/scripts/buildsystems/vcpkg.cmake

cmake --build . --config Release

Then, the executable will be available here /Open-PupilEXT-main/build/src/PupilEXT.

Note, the option -DCMAKE_TOOLCHAIN_FILE=3rdparty/vcpkg/scripts/buildsystems/vcpkg.cmak makes sure to use the submodule as package manager and download the C++ libraries defined in the vcpkg.json file. The -DVCPKG_TARGET_TRIPLET=x64-os option is necessary to let vcpkg know which triplet your need. On Windows you need to change the tripplet to -DVCPKG_TARGET_TRIPLET=x64-windows-static-md.

3.1 How to build from source on MacOS

Step 1: Download and install the Pylon Camera Softwware

Download the Pylon Camera Software Suite (*.dmg-File) from the Basler Website: https://www.baslerweb.com/de/vertrieb-support/downloads/downloads-software/

Step 2: Download and install QT

Download the QT from the website. Please install QT 5.15: https://www.qt.io/download-open-source?hsCtaTracking=9f6a2170-a938-42df-a8e2-a9f0b1d6cdce%7C6cb0de4f-9bb5-4778-ab02-bfb62735f3e5

Step 3: Install the package manager homebrew

Homebrew is a package manager for MacOS with which C++ libraries can be installed relatively easily via the terminal. Instructions on how to install Homebrew can be found here: https://brew.sh

To install homebrew , you can enter the following command in the MacOS terminal.

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Step 4: C++ Libraries

Now install the necessary C++ libraries for PupilEXT through homebrew. The Ceres library will be installed by OpenCV.

brew install cmake
brew install boost
brew install Eigen
brew install glog
brew install tbb
brew install opencv

Step 5: Download and build the spii library

An additional library called spii must be downloaded and built manually. This library is not included in Homebrew. First, go to the following GitHub repository and download it:

https://github.com/PetterS/spii

Open the downloaded folder spii-master with CLion. By default, CLion is set to debug mode. Therefore, the release option must be added. For this, go to CLion > Preferences > Build, Execution, Deployment in the toolbar. Then press the + symbol under CMake, which automatically adds the release mode. You can then switch to release in the top right-hand corner of the CLion toolbar. You can now build the project. Simply go to Build > Build Project.

Step 6: Add spii to PupilEXT

The source files of PupilEXT are located here in Github under the PupilEXT folder. Download it from GitHub and create a new folder called PupilEXT/external in the main PupilEXT folder. In external/ add another new folder called spii/.

In the folder PupilEXT/external/spii you need to copy the spii build created in step 5. First go to spii-master/cmake-build-release and copy the folder spii-master/cmake-build-release/lib to spii-master. Then copy all files inside the spii-master/ folder into PupilEXT/external/spii.

Step 7: Build PupilEXT from source

Now, open the PupilEXT project with CLion. In the file PupilEXT/CMakeLists.txt the paths must be updated so that the installed C++ libraries from step 4 can be correctly recognised. The complete content in PupilEXT/CMakeLists.txt can be removed and replaced by the following code snippet:

cmake_minimum_required(VERSION 3.15)
project(PupilEXT)
set(CMAKE_CXX_STANDARD 17)

set(CMAKE_AUTOMOC ON)
set(CMAKE_AUTORCC ON)
set(CMAKE_AUTOUIC ON)

if(CMAKE_VERSION VERSION_LESS "3.7.0")
    set(CMAKE_INCLUDE_CURRENT_DIR ON)
endif()

set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake)
set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} "/Users/papillon/Qt/5.15.2/clang_64")
set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} "/usr/local/Cellar/glog/0.4.0")
set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} "/usr/local/include/gflags")
set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} "/Library/Frameworks/pylon.framework")
set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} "/usr/local/Cellar/tbb/2020_U3_1")

set(SPII_INSTALL_DIR "/Users/papillon/Desktop/PupilEXT/external/spii")
set(spii_INCLUDE_DIRS ${SPII_INSTALL_DIR}/include)
set(GLOG_INCLUDE_DIR "/usr/local/Cellar/glog/0.4.0/include")
set(EIGEN_INCLUDE_DIR "/usr/local/Cellar/eigen/3.3.9/include/eigen3/Eigen")
set(EIGEN3_INCLUDE_DIR "/usr/local/include/eigen3")
SET("OpenCV_DIR" "/usr/local/Cellar/opencv/4.5.1_3/lib/cmake/opencv4")
SET("TBB_DIR" "/usr/local/Cellar/tbb/2020_U3_1/lib/cmake/TBB")

if(CMAKE_BUILD_TYPE STREQUAL Debug)
    set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} "/usr/local/share/ceres-solver")
else()
    set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} "/usr/local/share/ceres-solver")
endif()

set(PYLON_HOME "/Library/Frameworks/pylon.framework")
set(PYLON_INCLUDE_DIR "/Library/Frameworks/pylon.framework/Headers")

find_package(Qt5 COMPONENTS Widgets Concurrent SerialPort Charts Svg PrintSupport Network Xml REQUIRED)
find_package(OpenCV REQUIRED PATHS "/usr/local/Cellar/opencv/4.5.1_3")
find_package(Boost 1.72 REQUIRED)
find_package(TBB REQUIRED PATHS "${PROJECT_SOURCE_DIR}/external/tbb")
find_package(Eigen3 REQUIRED )
find_package(Ceres REQUIRED)
find_package(Pylon REQUIRED)
find_package(OpenGL REQUIRED)

set(TBB_LIBRARY_DEBUG "/usr/local/include/tbb")
set(TBB_LIBRARY_RELEASE "/usr/local/include/tbb")

find_library (spii_LIBRARY_RELEASE
        spii
        PATHS ${SPII_INSTALL_DIR}/lib/)
find_library (meschach_LIBRARY_RELEASE
        meschach
        PATHS ${SPII_INSTALL_DIR}/lib/)
if (spii_LIBRARY_RELEASE AND meschach_LIBRARY_RELEASE)
    set(spii_LIBRARIES ${spii_LIBRARY_RELEASE} ${meschach_LIBRARY_RELEASE})
else()
    set(spii_LIBRARIES "")
endif()

include_directories(${Qt5Core_INCLUDE_DIRS}
        ${Qt5Widgets_INCLUDE_DIRS}
        ${Qt5Concurrent_INCLUDE_DIRS}
        ${Qt5SerialPort_INCLUDE_DIRS}
        ${Qt5Charts_INCLUDE_DIRS}
        ${Qt5Svg_INCLUDE_DIRS}
        ${Qt5PrintSupport_INCLUDE_DIRS}
        ${Qt5Network_INCLUDE_DIRS}
        ${Qt5Xml_INCLUDE_DIRS}
        ${OpenCV_INCLUDE_DIRS}
        ${Boost_INCLUDE_DIRS}
        ${TBB_INCLUDE_DIR}
        ${spii_INCLUDE_DIRS}
        ${EIGEN_INCLUDE_DIR}
        ${CERES_INCLUDE_DIRS}
        ${PYLON_INCLUDE_DIR}
        "singleeyefitter")

add_subdirectory (src)
add_subdirectory (singleeyefitter)

message(STATUS "")
message(STATUS "spii_LIBRARIES:\"${spii_LIBRARIES}\"")
message(STATUS "--- Include directories ---" )
message(STATUS " QT5Core_INCLUDE_DIRS: ${Qt5Core_INCLUDE_DIRS}")
message(STATUS " Qt5Concurrent_INCLUDES: ${Qt5Concurrent_INCLUDE_DIRS}")
message(STATUS " Qt5SerialPort_INCLUDES: ${Qt5SerialPort_INCLUDE_DIRS}")
message(STATUS " Qt5Charts_INCLUDES: ${Qt5Charts_INCLUDE_DIRS}")
message(STATUS " Qt5Svg_INCLUDES: ${Qt5Svg_INCLUDE_DIRS}")
message(STATUS " Qt5PrintSupport_INCLUDES: ${Qt5PrintSupport_INCLUDE_DIRS}")
message(STATUS " Qt5Network_INCLUDES: ${Qt5Network_INCLUDE_DIRS}")
message(STATUS " Qt5Xml_INCLUDES: ${Qt5Xml_INCLUDE_DIRS}")

message(STATUS " OpenCV_INCLUDE_DIRS: ${OpenCV_INCLUDE_DIRS}" )
message(STATUS " Boost_INCLUDE_DIRS: ${Boost_INCLUDE_DIRS}" )
message(STATUS " TBB_INCLUDE_DIRS: ${TBB_INCLUDE_DIR}" )
message(STATUS " spii_INCLUDE_DIRS: ${spii_INCLUDE_DIRS}" )
message(STATUS " EIGEN_INCLUDE_DIR: ${EIGEN_INCLUDE_DIR}" )
message(STATUS " CERES_INCLUDE_DIRS: ${CERES_INCLUDE_DIRS}" )
message(STATUS " PYLON_INCLUDE_DIRS: ${PYLON_INCLUDE_DIR}" )
message(STATUS "---------------------------" )
message(STATUS "")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native -O3")

Make sure that all folder paths in the CMakelist.txt are adapted to your system. For instance, the path /Users/papillonmac/Qt/5.15.0/clang_64 must be changed with the name of your user name and your specific QT version installed on your PC.

The described changes to the Pylon library in this section can be skipped, as we included in the updated CMakelists.txt the following code for MacOS:

set(PYLON_INCLUDE_DIR ${PYLON_INCLUDE_DIR} "/Library/Frameworks/pylon.framework/Headers")
    set(PYLON_INCLUDE_DIR ${PYLON_INCLUDE_DIR} "/Library/Frameworks/pylon.framework/Headers/GenICam")

Old description (not needed):

The last step is to change something in the Pylon library; otherwise, the library will not be found properly. For this, open the following folder on your computer: /Library/Frameworks/pylon.framework/Versions/A/Headers/GenICam. All files in this folder must be copied to /Library/Frameworks/pylon.framework/Versions/A/Headers.

Now, you should be able to start PupilEXT properly in CLion. Please remember to use the release option as in step 5; otherwise, PupilEXT will run in debug mode and will be significantly slower.

3.2 How to build from source on Windows 10

Step 1: Install Visual Studio 2019

C++ MFC must be installed during the installation. Additionally, the English language package must be included. Visual Studio can be downloaded from the following page:

https://visualstudio.microsoft.com/downloads/

Step 2: Download and install the Pylon Camera Software

Download the Pylon Camera Software Suite (*.dmg) from the Basler Website: https://www.baslerweb.com/de/vertrieb-support/downloads/downloads-software/

Step 3: Download and install QT

Download the QT from the website. Please install QT 5.15. You need to add msvc2017_64 during the installation: https://www.qt.io/download-open-source?hsCtaTracking=9f6a2170-a938-42df-a8e2-a9f0b1d6cdce%7C6cb0de4f-9bb5-4778-ab02-bfb62735f3e5

Step 4: Install the C++ package manager

There is a C++ package manager from Microsoft for Windows, making it relatively easy to download libraries. For this, install the program vcpkg. The instructions on how to install the package manager can be found on the following page:

https://docs.microsoft.com/de-de/cpp/build/install-vcpkg?view=msvc-160&tabs=windows

To install vcpkg type in your console the following commands:

git clone https://github.com/Microsoft/vcpkg.git
cd vcpkg
.\bootstrap-vcpkg.bat

Step 5: Install the C++ Librarys

Go to your console and use the following commands to install the C++ libraries:

vcpkg install boost:x64-windows
vcpkg install Eigen:x64-windows
vcpkg install ceres:x64-windows
vcpkg install glog:x64-windows
vcpkg install opencv:x64-windows
vcpkg install tbb:x64-windows

Step 6: Download and build spii

The spii library is not included in vcpkg. You need to build it manually. First, go to the following page and download the spii library from GitHub:

https://github.com/PetterS/spii

Then CLion can be used to open and build the spii library. Make sure that you use the 64 bit architecture. Then the folder spii-master/cmake-build-release/lib can be copied into the main folder spii-master/. Lastly, copy the files inside spii-master/ to PupilEXT/external/spii.

Step 7: Prepare the CMakelists file

You can add the following code snippet to the file PupilEXT/CMakeLists.txt to let PupilEXT recognize vcpkg libraries. Make sure to adjust the appropriate paths and version numbers.

cmake_minimum_required(VERSION 3.15)
project(PupilEXT)

set(CMAKE_AUTOMOC ON)
set(CMAKE_AUTORCC ON)
set(CMAKE_AUTOUIC ON)
if(CMAKE_VERSION VERSION_LESS "3.7.0")
    set(CMAKE_INCLUDE_CURRENT_DIR ON)
endif()

set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake)
set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} "C:/Qt/Qt5.13.1/5.10.0/msvc2017_64")
set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} "C:/vcpkg/installed/x64-windows")
set(GLOG_INCLUDE_DIR "C:/vcpkg/installed/x64-windows/include")
if(CMAKE_BUILD_TYPE STREQUAL Debug)
    set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} "C:/vcpkg/installed/x64-windows/debug")
else()
    set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} "C:/vcpkg/installed/x64-windows/include")
endif()

set(TBB_INCLUDE_DIR "C:/vcpkg/installed/x64-windows/include/tbb")
set(SPII_INSTALL_DIR "${PROJECT_SOURCE_DIR}/external/spii")
set(spii_INCLUDE_DIRS ${SPII_INSTALL_DIR}/include)
set(PYLON_HOME "C:/Program Files/Basler/pylon 6/Development/")
find_package(Qt5 COMPONENTS Widgets SerialPort Charts Svg PrintSupport Network Xml REQUIRED)
find_package(OpenCV REQUIRED)
find_package(Boost 1.72 REQUIRED)
find_package(TBB REQUIRED PATHS "${PROJECT_SOURCE_DIR}/external/tbb")
find_package(Eigen3 REQUIRED )
find_package(Ceres CONFIG REQUIRED)
find_package(Pylon REQUIRED)
set(TBB_LIBRARY_DEBUG "${PROJECT_SOURCE_DIR}/external/tbb/lib/intel64")
set(TBB_LIBRARY_RELEASE "${PROJECT_SOURCE_DIR}/external/tbb/lib/intel64")

find_library (spii_LIBRARY_RELEASE
        spii
        PATHS ${SPII_INSTALL_DIR}/lib/)
find_library (meschach_LIBRARY_RELEASE
        meschach
        PATHS ${SPII_INSTALL_DIR}/lib/)
if (spii_LIBRARY_RELEASE AND meschach_LIBRARY_RELEASE)
    set(spii_LIBRARIES ${spii_LIBRARY_RELEASE} ${meschach_LIBRARY_RELEASE})
else()
    set(spii_LIBRARIES "")
endif()

include_directories(${Qt5Core_INCLUDE_DIRS}
        ${Qt5Widgets_INCLUDE_DIRS}
        ${Qt5Concurrent_INCLUDE_DIRS}
        ${Qt5SerialPort_INCLUDE_DIRS}
        ${Qt5Charts_INCLUDE_DIRS}
        ${Qt5Svg_INCLUDE_DIRS}
        ${Qt5PrintSupport_INCLUDE_DIRS}
        ${Qt5Network_INCLUDE_DIRS}
        ${Qt5Xml_INCLUDE_DIRS}
        ${OpenCV_INCLUDE_DIRS}
        ${Boost_INCLUDE_DIRS}
        ${TBB_INCLUDE_DIR}
        ${spii_INCLUDE_DIRS}
        ${EIGEN_INCLUDE_DIR}
        ${CERES_INCLUDE_DIRS}
        ${PYLON_INCLUDE_DIR}
        "singleeyefitter")

add_subdirectory (src)
add_subdirectory (singleeyefitter)

message(STATUS "")
message(STATUS "spii_LIBRARIES:\"${spii_LIBRARIES}\"")
message(STATUS "--- Include directories ---" )
message(STATUS " QT5Core_INCLUDE_DIRS: ${Qt5Core_INCLUDE_DIRS}")
message(STATUS " Qt5Concurrent_INCLUDES: ${Qt5Concurrent_INCLUDE_DIRS}")
message(STATUS " Qt5SerialPort_INCLUDES: ${Qt5SerialPort_INCLUDE_DIRS}")
message(STATUS " Qt5Charts_INCLUDES: ${Qt5Charts_INCLUDE_DIRS}")
message(STATUS " Qt5Svg_INCLUDES: ${Qt5Svg_INCLUDE_DIRS}")
message(STATUS " Qt5PrintSupport_INCLUDES: ${Qt5PrintSupport_INCLUDE_DIRS}")
message(STATUS " Qt5Network_INCLUDES: ${Qt5Network_INCLUDE_DIRS}")
message(STATUS " Qt5Xml_INCLUDES: ${Qt5Xml_INCLUDE_DIRS}")

message(STATUS " OpenCV_INCLUDE_DIRS: ${OpenCV_INCLUDE_DIRS}" )
message(STATUS " Boost_INCLUDE_DIRS: ${Boost_INCLUDE_DIRS}" )
message(STATUS " TBB_INCLUDE_DIRS: ${TBB_INCLUDE_DIR}" )
message(STATUS " spii_INCLUDE_DIRS: ${spii_INCLUDE_DIRS}" )
message(STATUS " EIGEN_INCLUDE_DIR: ${EIGEN_INCLUDE_DIR}" )
message(STATUS " CERES_INCLUDE_DIRS: ${CERES_INCLUDE_DIRS}" )
message(STATUS " Pylon_INCLUDE_DIRS: ${PYLON_INCLUDE_DIR}" )
message(STATUS "---------------------------" )
message(STATUS "")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native -O3")

Step 8: Environment variables

Add the bin folder of vcpkg and QT to the environment variables of Windows; otherwise, the libraries will not be found.

Step 9: Build PupilEXT with CLion

Before the programme can be build, some settings must be made in CLion:

File > Setting > Build, Execution, Deoployment > CMAKE under CMAKE options add the following parameter: --config Debug -DVCPKG_TARGET_TRIPLET=x64-windows -DCMAKE_TOOLCHAIN_FILE=C:/vcpkg/scripts/buildsystems/vcpkg.cmake
Then press the plus sign to add the release configuration. Add the following parameters to the release options:: --config Release -DVCPKG_TARGET_TRIPLET=x64-windows -DCMAKE_TOOLCHAIN_FILE=C:/vcpkg/scripts/buildsystems/vcpkg.cmake
The build architecture must be changed to amd64 under Toolchain, as the vcpkg libraries were also installed with 64 bit.

Next, the bin folders must be added to the path of CLION, as these are independent of the Windows environment variables. Under Run > Edit Configuration the paths to VCPKG and QT can be added:

C:\Qt\Qt5.13.1\5.10.0\msvc2017_64\bin
C:\vcpkg\installed\x64-windows\bin

In order to start the programme, the SPII DLL must be added to PupilEXT\cmake-build-debug\src. If everything has been done correctly, you can now press Start and the software should open without any issues.

4. Misc

Camera emulation For debugging porpuses, the Pylon SDK supports emulating camera devices that are then displayed as physical cameras in the PupilExt software. To activate the camera emulation, the system environment variable "PYLON_CAMEMU" needs to be set. The number of available emulator devices can be controlled by exporting the PYLON_CAMEMU environment variable. For example, export PYLON_CAMEMU=2.

5. Known issues

see here https://github.com/openPupil/Open-PupilEXT/issues

6. Citation

Please consider to cite our work if you find this repository or our results useful for your research:

B. Zandi, M. Lode, A. Herzog, G. Sakas, and T. Q. Khanh, “PupilEXT: Flexible Open-Source Platform for High-Resolution Pupillometry in Vision Research,” Front. Neurosci., vol. 15, Jun. 2021, doi: 10.3389/fnins.2021.676220.

@Article{10.3389/fnins.2021.676220,
AUTHOR = {Zandi, Babak and Lode, Moritz and Herzog, Alexander and Sakas, Georgios and Khanh, Tran Quoc},
TITLE = {PupilEXT: Flexible Open-Source Platform for High-Resolution Pupillometry in Vision Research},
JOURNAL = {Frontiers in Neuroscience},
VOLUME={15},      
PAGES={603},     
YEAR={2021}, 
URL={https://www.frontiersin.org/article/10.3389/fnins.2021.676220},
DOI={10.3389/fnins.2021.676220},    
ISSN={1662-453X}}

Additional citation for Release v0.1.2 beta:

G. L. Bényei, A. B. Boncsér, P. Pajkossy, "Promise of open-source, low-cost pupillometry - Contribution to the PupilEXT platform," ECEM Conference Poster, Aug. 2024, doi: 10.13140/RG.2.2.33761.93284.

@Misc{10.13140/RG.2.2.33761.93284,
AUTHOR = {Gábor L., Bényei and Attila B., Boncsér and Péter, Pajkossy},
TITLE = {Promise of open-source, low-cost pupillometry - Contribution to the PupilEXT platform},    
YEAR={2024}, 
URL={https://www.doi.org/10.13140/RG.2.2.33761.93284},
DOI={10.13140/RG.2.2.33761.93284}}

7. References

[1] Dongheng Li and Derrick J. Parkhurst. Starburst: A robust algorithm for video-based eye tracking. IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR), September 2005.

[2] Lech Swirski, Andreas Bulling, and Neil Dodgson. Robust real-time pupil tracking in highly off-axis images. In Proceedings - 2012 ACM Symposium on Eye Tracking Research and Applications (ETRA), pages 173–176, 2012.

[3] Wolfgang Fuhl, Thomas Kübler, Katrin Sippel, Wolfgang Rosenstiel, and Enkelejda Kasneci. Excuse: robust pupil detection in real-world scenarios. In International Conference on Computer Analysis of Images and Patterns, pages 39–51. Springer, 2015.

[4] Wolfgang Fuhl, Thiago C. Santini, Thomas Kübler, and Enkelejda Kasneci. ElSe: Ellipse selection for robust pupil detection in real-world environments. In Proceedings - 2016 ACM Symposium on Eye Tracking Research and Applications (ETRA), volume 14, pages 123–130, 2016.

[5] Thiago Santini, Wolfgang Fuhl, and Enkelejda Kasneci. PuRe: Robust pupil detection for real-time pervasive eye tracking. Computer Vision and Image Understanding, 170:40–50, 2018.

[6] Thiago Santini, Wolfgang Fuhl, and Enkelejda Kasneci. PuReST: Robust pupil tracking for real-time pervasive eye tracking. In Proceedings - 2018 ACM Symposium on Eye Tracking Research and Applications (ETRA). ACM, 2018.

[7] Thiago Santini, Wolfgang Fuhl, David Geisler and Enkelejda Kasneci. EyeRecToo: Open-source Software for Real-time Pervasive Head-mounted Eye Tracking. VISIGRAPP 2017.

8. Open source projects inside PupilEXT

PupilEXT integrates several open source libraries. This document provides a list of the used libraries. The respective licenses of the libraries are provided as *.txt file in in the subfolder 3rdparty/PupilEXT_Third_Party_Licenses.

List of Pupil Detection Libraries

EyeRecToo is an open-source eye tracking software for head-mounted eye tracker and integrates the most advanced state-of-the-art open-source pupil detection algorithms. We used the implementation of the EyeRecToo’s pupil class and the integrated detection methods for PupilEXT. (License: Copyright (c) 2018, Thiago Santini / University of Tübingen). License: For academic and non-commercial use only (Link License | Project Page).

PuRe Thiago Santini, Wolfgang Fuhl, Enkelejda Kasneci, PuRe: Robust pupil detection for real-time pervasive eye tracking. Computer Vision and Image Understanding. 2018, ISSN 1077-3142. https://doi.org/10.1016/j.cviu.2018.02.002. Part of the EyeRecToo software. Copyright (c) 2018, Thiago Santini, University of Tübingen. License: For non-commercial purposes only (Link).

PuReST Thiago Santini, Wolfgang Fuhl, Enkelejda Kasneci. PuReST: Robust pupil tracking for real-time pervasive eye tracking. Symposium on Eye Tracking Research and Applications (ETRA). 2018. https://doi.org/10.1145/3204493.3204578. Part of the EyeRecToo software. Copyright (c) 2018, Thiago Santini, University of Tübingen. License: For non-commercial purposes (Link).

ElSe Wolfgang Fuhl, Thiago Santini, Thomas Kübler, Enkelejda Kasneci. ElSe: Ellipse Selection for Robust Pupil Detection in Real-World Environments. ETRA 2016 : Eye Tracking Research and Application. 2016. Part of the EyeRecToo software. Copyright (c) 2018, Thiago Santini, University of Tübingen. License: For non-comercial use only (Link).

ExCuSe Wolfgang Fuhl, Thomas Kübler, Katrin Simpel, Wolfgang Rosenstiel, Enkelejda Kasneci. ExCuSe: Robust Pupil Detection in Real-World Scenarios. CAIP 2015 : Computer Analysis of Images and Patterns. 2015. Part of the EyeRecToo software. Copyright (c) 2018, Thiago Santini, University of Tübingen. License: For non-comercial use only (Link).

Starburst Dongheng Li, Winfield, D., Parkhurst, D. J. Starburst: A hybrid algorithm for video-based eye tracking combining feature-based and model-based approaches. in 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR’05) - Workshops vol. 3 79–79 (IEEE, 2005). https://doi.org/10.1109/CVPR.2005.531. Based on the cvEyeTracker Version 1.2.5 implementation. License: GNU General Public License (Link)

Swirski2D Lech Swirski, Andreas Bulling, Neil Dodgson. Robust real-time pupil tracking in highly off-axis images. ETRA 2012: Proceedings of the Symposium on Eye Tracking Research and Applications. 2012. https://doi.org/10.1145/2168556.2168585. License: MIT License, Copyright (c) 2014 Lech Swirski (Link)

Swirski2D Lech Swirski, Neil Dodgson. A fully-automatic, temporal approach to single camera, glint-free 3D eye model fitting. Proceedings of ECEM 2013. 2013. License: MIT License, Copyright (c) 2014 Lech Swirski (Link)

List of Software Libraries

QT is an open-source widget toolkit for creating graphical user interfaces as well as cross-platform applications that run on various software and hardware platforms such as Linux, Windows, macOS, Android or embedded systems. (License: GPL 3.0)

QCustomPlot is a Qt C++ widget for plotting and data visualization. It has no further dependencies and is well documented. (License: GPL 3.0)

OpenCV is a highly optimized computer vision library with focus on real-time applications. In this repository it is used for image manipulation and plotting of ellipse pupil detections. (License: Apache 2 / BSD)

Glog is a library for logging. (License)

Boost is a set of various C++ libraries for processing tasks. (License)

Ceres-Solver is a optimisation library. (License)

Eigen is a library for linear algebra. (License)

Spii is a library for optimisation. (License)

Tbb is for parallel programming. (License)

Gflags is a library for comandline processing. (License)

List of used graphics, icons, and helper scripts

Breeze Icons is a set of icons. (License)

The following icon files are modifications of existing icons from the KDE Breeze icon set: 1cam1pup.svg, 1cam2pup.svg, 1cam1pup.svg, 1Mcam1pup.svg, 2cam1pup.svg, 2cam2pup.svg, 2cam2pupNS.svg, media-record-green.svg, camera-video-stereo.svg, crosshairs-gaze-calibration.svg, crosshairs-gaze-validation.svg. These modified files were made by contributor Gábor Bényei, and can be found in the icons folder as resources, licensed in accordance to KDE Breeze license (GNU LESSER GENERAL PUBLIC LICENSE Version 3).

The following icon files are the work of Gábor Bényei, and are declared public domain: computer-connection.svg, equals1b.svg, plus1b.svg, messageEmpty.svg, rs232.svg.

The OpenCV logo (OpenCV_Logo_with_text_svg_version.svg) is the work of Adi Shavit, under BSD license. License text and source: https://commons.wikimedia.org/wiki/File:OpenCV_Logo_with_text_svg_version.svg, last accessed 2024.08.16. 09:36 CET

The Qt logo (Qt_logo_2016.svg) is the work of The Qt Project, and is public domain. License reference and source: https://commons.wikimedia.org/wiki/File:Qt_logo_2016.svg, last accessed 2024.08.16 09:36 CET

The script make_dmg_from_app.command is a customized version of a dmg maker script from Andy Maloney's blog: https://asmaloney.com/2013/07/howto/packaging-a-mac-os-x-application-using-a-dmg/, last accessed 2024.08.23. 06:50 CET

PupilEXT_dmg_background contains the PupilEXT logo, which is the work of the authors of PupilEXT v0.1.1, and was edited by Gabor Benyei to make the installer background image

9. Acknowledgment

We thank the German Research Foundation (DFG) by funding the research (grant number: 450636577).

This project was made possible by the outstanding previous published open-source projects in the field of pupil detection and eye-tracking. Therefore, we would like to thank the authors of the ground-breaking algorithms PuRe, PuReST, ElSe, ExCuSe, Starburst and Swirski, who made their methods available to the public. Namely, we have to thank Wolfgang Fuhl, Thiago Santini, Thomas Kübler, Enkelejda Kasneci, Katrin Sippel, Wolfgang Rosenstiel, Dongheng Li, D. Winfield, D. Parkhurst, Lech Swirski, Andreas Bulling and Neil Dodgson for their open-source contributions which are part of PupilEXT. Additionally, we would like to thank the outstanding developers of the software EyeRecToo, whose open-source eye-tracking software inspired us for this work. We used the implementation of the EyeRecToo’s pupil class and the integrated detection methods for PupilEXT.

We appreciate the contributions of Paul Myland, who supported us as a co-supervisor in a bachelor thesis, which topically worked on one part of this project. We highly welcome the contribution of Mohammad Zidan for the mechanical construction of the stereo camera system and the NIR illumination, which was done during his bachelor thesis, supervised by Babak Zandi. Finally, we would like to thank Felix Wirth and Thomas Lautenschläger who joined us as student assistants in the initial phase of the project.

10. License

The work's content (Paper) is licensed under a Creative Commons Attribution 4.0 International License.

The embedded code for the STM32 Nucleo is licensed under the MIT license.

The software PupilEXT is licensed under GNU General Public License v.3.0., Copyright (c) 2021 Technical University of Darmstadt. The pupil detection functionalities of PupilEXT are for academic and non-commercial use only. Please note that third-party libraries used in PupilEXT may be distributed under other open-source licenses. Please read the above section 8: Open source projects inside PupilEXT.

This program is distributed in the hope that it will be useful, but without any warranty, without even the implied warranty of fitness for a particular purpose.

Name		Name	Last commit message	Last commit date
Latest commit History 164 Commits
.vscode		.vscode
3rdparty		3rdparty
Community		Community
Misc		Misc
cmake		cmake
icons		icons
singleeyefitter		singleeyefitter
src		src
.gitignore		.gitignore
.gitmodules		.gitmodules
CMakeLists.txt		CMakeLists.txt
PupilExt.qrc		PupilExt.qrc
PupilExt.rc		PupilExt.rc
README.md		README.md
Third_Party_Licenses.html		Third_Party_Licenses.html
icon.icns		icon.icns
icon.ico		icon.ico
icon.svg		icon.svg
qt5.natvis		qt5.natvis
vcpkg.json		vcpkg.json

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PupilEXT: flexible open-source platform for high resolution pupillometry in vision research

1. Overview

1.1 Pupillometry setup configuations

1.2 Hardware and software requirements

2. Getting started: The easy way

2.1. Installation on MacOS (MacOS 12.7.6 or later)

2.2. Installation on Windows 10 (64 bit)

2.3. Setup the microcontroller for the stereo camera configuration

2.4. Demo dataset for offline analysis

2.5 Notes about pupil detection accuracy

2.5. How to use PupilEXT ?

Opening a single camera or stereo setup

Opening an existing image recording

Making an image recording

Calibrating for camera image undistortion and px-mm mapping

Setting up pupil detection

Using pupil tracking

Making data recordings

Streaming data

A note on reproducibility

2.6. Integrating PupilEXT into a cognitive science experiment

2.7. Starting PupilEXT with executable arguments

3. Build PupilEXT from source: The advanced way

3.0 Build PupilEXT with vcpkg manifest (recommended)

3.1 How to build from source on MacOS

3.2 How to build from source on Windows 10

4. Misc

5. Known issues

6. Citation

Additional citation for Release v0.1.2 beta:

7. References

8. Open source projects inside PupilEXT

List of Pupil Detection Libraries

List of Software Libraries

List of used graphics, icons, and helper scripts

9. Acknowledgment

10. License

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