Vision Experiment Manager

Vision Experiment Manager is a Python based software framework for automating experiments related to studying vision at retinal and cortical levels. Several applications are depending on the framework: visual stimulation, behavioral control and online analysis tools. Besides experiment automation, it focuses on preprocessing or quick analysis of data to give an immediate feedback to the experimenter and help further analysis at higher levels.

 

The framework’s applications can be interfaced to several measurement methods: Calcium imaging, single patch electrode or multielectrode array recordings. Screen/projector is the most common stimulation device but Lasers and LED light sources are also supported.

 

Vision Experiment Manager is being developed in Botond Roska’s research group in Friedrich Miescher Institute. The foundations of the framework were designed with Daniel Hillier.

 

Supported Experimental Setups

  • Femtonics Rollercoaster (RC) two photon microscope
  • Femtonics Acoustooptic (AO) two photon microscope
  • Retinal two photon microscope
  • Multichannel Systems multielectrode array
  • Hidens multielectrode array
  • Behavioral setup
  • Cortical ultrasound setup (under development)

 

Contribution to Publications

The following research projects used Vision Experiment Manager:

Antonia Drinnenberg et al.
How diverse retinal functions arise from feedback at the first visual synapse
Neuron, 2018

Keisuke Yonehara et al.
Congenital Nystagmus Gene FRMD7 Is Necessary for Establishing a Neuronal Circuit Asymmetry for Direction Selectivity.
Neuron, 2016

Karl Farrow et al.
Ambient Illumination Toggles a Neuronal Circuit Switch in the Retina and Visual Perception at Cone Threshold
Neuron, 2013

Behavioral Experiment Software

Controls mouse behavioral experiment and visualizes experiment results. The behavioral protocol is run by a microcontroller based real-time environment.

Calcium Imaging Online Analysis

The main user interface of Vision Experiment Manager has the capability of analyzing Calcium Imaging data. The datafiles can be opened for automatic or manual cell detection. Data can be exported to Matlab mat file.

Vision Experiment Manager for Femtonics RC Microscope

The early version of the main user interface of Vision Experiment Manager has limited analysis functions. It focuses on controlling Femtonics RC Microscope and visual stimulation software. It handles scan regions, displays online analysis status. It has access to motorized stage and goniometer that helps aligning the sample. It is used for in-vivo cortical Calcium Imaging of mice.

Visual Stimulation

Generates various visual patterns for retinal or visual cortex stimulation: Moving grating, moving bars, natural stimuli, checkerboard, multiple dots.

Additional features:

  • Integrated with Vision Experiment Control, stimulus start is triggered via zmq
  • Interface to NI Data acquisition cards enabling control of various external stimulation devices like lasers, led sources.
  • Stimulation files are in Python syntax
  • Experiment control, trigger generation
  • Filterwheel control
  • Runs on Windows xp/7/10, Mac and Ubuntu Linux

Daniel Hillier, Michele Fiscella, Antonia Drinnenberg, Stuart Trenholm, Santiago B Rompani, Zoltan Raics, Gergely Katona, Josephine Juettner, Andreas Hierlemann, Balazs Rozsa & Botond Roska Causal evidence for retina-dependent and -independent visual motion computations in mouse cortex Nature Neuroscience, 2017

A Wertz, S Trenholm, K Yonehara, D Hillier, Z Raics, M Leinweber, G Szalay, A Ghanem, G Keller, B Rozsa, K Conzelmann, B Roska,
Single-cell-initiated monosynaptic tracing reveals layer-specific cortical network modules
Science, 2015

T Szikra, S Trenholm, A Drinnenberg, J Juttner, Z Raics, K Farrow, M Biel, G Awatramani, D Clark, J Sahel, R da Silveira, B Roska,
Rods in daylight act as relay cells for cone-driven horizontal cell-mediated surround inhibition
Nature Neuroscience, 2014

Two Photon Imaging

Controls two photon microscopy setup

  • Two photon imaging
  • Calcium imaging
  • Infrared camera control
  • Stage control
  • Advanced visualization of image channels including user lookup tables and many filters.
  • Two photon and infrared image can be overlaid
  • Z stack
  • Can be triggered via network from Vision Experiment Manager
  • Written in LabVIEW

Contribution to Publications

AkihiroMatsumoto et al.
Direction selectivity in retinal bipolar cell axon terminals
Neuron, 2021

Emilie Macé et al.
Targeting Channelrhodopsin-2 to ON-bipolar Cells With Vitreally Administered AAV Restores ON and OFF Visual Responses in Blind Mice
Molecular Therapy, 2015

Keisuke Yonehara et al.
The First Stage of Cardinal Direction Selectivity Is Localized to the Dendrites of Retinal Ganglion Cells
Neuron, 2013

Home Made Software

 

Ultrasound Radar (2017)

This application is used for testing the HC-SR04 ultrasound range finder. It controls servos which adjust the rotation and tilt of the HC-SR04. A map is formed from the measured distances and it is displayed. Source code is on Github

Adel Monitor (2016)

A Flask and Sqlite based web application for tracking baby’s feeding times, weight gain and sleep time. Statistics are displayed on plots helping to identify feeding and sleep patterns. Source code is available at Github.

HARDWARE

Vision Experiment Manager

Vision Experiment Manager is a Python based software framework for automating experiments related to studying vision at retinal and cortical levels. Several applications are depending on the framework: visual stimulation, behavioral control and online analysis tools. Besides experiment automation, it focuses on preprocessing or quick analysis of data to give an immediate feedback to the experimenter and help further analysis at higher levels.

 

The framework’s applications can be interfaced to several measurement methods: Calcium imaging, single patch electrode or multielectrode array recordings. Screen/projector is the most common stimulation device but Lasers and LED light sources are also supported.

 

Vision Experiment Manager is being developed in Botond Roska’s research group in Friedrich Miescher Institute. The foundations of the framework were designed with Daniel Hillier.

 

Supported Experimental Setups

  • Femtonics Rollercoaster (RC) two photon microscope
  • Femtonics Acoustooptic (AO) two photon microscope
  • Retinal two photon microscope
  • Multichannel Systems multielectrode array
  • Hidens multielectrode array
  • Behavioral setup
  • Cortical ultrasound setup (under development)

 

Contribution to Publications

The following research projects used Vision Experiment Manager:

Antonia Drinnenberg et al.
How diverse retinal functions arise from feedback at the first visual synapse
Neuron, 2018

Keisuke Yonehara et al.
Congenital Nystagmus Gene FRMD7 Is Necessary for Establishing a Neuronal Circuit Asymmetry for Direction Selectivity.
Neuron, 2016

Karl Farrow et al.
Ambient Illumination Toggles a Neuronal Circuit Switch in the Retina and Visual Perception at Cone Threshold
Neuron, 2013

Behavioral Experiment Software

Controls mouse behavioral experiment and visualizes experiment results. The behavioral protocol is run by a microcontroller based real-time environment.

Calcium Imaging Online Analysis

The main user interface of Vision Experiment Manager has the capability of analyzing Calcium Imaging data. The datafiles can be opened for automatic or manual cell detection. Data can be exported to Matlab mat file.

Vision Experiment Manager for Femtonics RC Microscope

The early version of the main user interface of Vision Experiment Manager has limited analysis functions. It focuses on controlling Femtonics RC Microscope and visual stimulation software. It handles scan regions, displays online analysis status. It has access to motorized stage and goniometer that helps aligning the sample. It is used for in-vivo cortical Calcium Imaging of mice.

Visual Stimulation

Generates various visual patterns for retinal or visual cortex stimulation: Moving grating, moving bars, natural stimuli, checkerboard, multiple dots.

Additional features:

  • Integrated with Vision Experiment Control, stimulus start is triggered via zmq
  • Interface to NI Data acquisition cards enabling control of various external stimulation devices like lasers, led sources.
  • Stimulation files are in Python syntax
  • Experiment control, trigger generation
  • Filterwheel control
  • Runs on Windows xp/7/10, Mac and Ubuntu Linux

Daniel Hillier, Michele Fiscella, Antonia Drinnenberg, Stuart Trenholm, Santiago B Rompani, Zoltan Raics, Gergely Katona, Josephine Juettner, Andreas Hierlemann, Balazs Rozsa & Botond Roska Causal evidence for retina-dependent and -independent visual motion computations in mouse cortex Nature Neuroscience, 2017

A Wertz, S Trenholm, K Yonehara, D Hillier, Z Raics, M Leinweber, G Szalay, A Ghanem, G Keller, B Rozsa, K Conzelmann, B Roska,
Single-cell-initiated monosynaptic tracing reveals layer-specific cortical network modules
Science, 2015

T Szikra, S Trenholm, A Drinnenberg, J Juttner, Z Raics, K Farrow, M Biel, G Awatramani, D Clark, J Sahel, R da Silveira, B Roska,
Rods in daylight act as relay cells for cone-driven horizontal cell-mediated surround inhibition
Nature Neuroscience, 2014

Two Photon Imaging

Controls two photon microscopy setup

  • Two photon imaging
  • Calcium imaging
  • Infrared camera control
  • Stage control
  • Advanced visualization of image channels including user lookup tables and many filters.
  • Two photon and infrared image can be overlaid
  • Z stack
  • Can be triggered via network from Vision Experiment Manager
  • Written in LabVIEW

Contribution to Publications

AkihiroMatsumoto et al.
Direction selectivity in retinal bipolar cell axon terminals
Neuron, 2021

Emilie Macé et al.
Targeting Channelrhodopsin-2 to ON-bipolar Cells With Vitreally Administered AAV Restores ON and OFF Visual Responses in Blind Mice
Molecular Therapy, 2015

Keisuke Yonehara et al.
The First Stage of Cardinal Direction Selectivity Is Localized to the Dendrites of Retinal Ganglion Cells
Neuron, 2013

Home Made Software

 

Ultrasound Radar (2017)

This application is used for testing the HC-SR04 ultrasound range finder. It controls servos which adjust the rotation and tilt of the HC-SR04. A map is formed from the measured distances and it is displayed. Source code is on Github

Adel Monitor (2016)

A Flask and Sqlite based web application for tracking baby’s feeding times, weight gain and sleep time. Statistics are displayed on plots helping to identify feeding and sleep patterns. Source code is available at Github.

PUBLICATIONS

Zoltán Raics

CEO, Software Engineer

Balázs Gyöngyösi

Electronic Engineer

Kinga Futó, PhD

Biologist

Péter Raics, PhD

Physicist

REFERENCES

PUBLICATIONS

Dasha Nelidova, Rei K Morikawa, Cameron S Cowan, Zoltan Raics, David Goldblum, Hendrik P N Scholl, Tamas Szikra, Arnold Szabo, Daniel Hillier, Botond Roska: Restoring light sensitivity using tunable near-infrared sensors Science Vol. 368, Issue 6495, pp. 1108-1113, 2020

Daniel Hillier, Michele Fiscella, Antonia Drinnenberg, Stuart Trenholm, Santiago B Rompani, Zoltan Raics, Gergely Katona, Josephine Juettner, Andreas Hierlemann, Balazs Rozsa & Botond Roska: Causal evidence for retina-dependent and -independent visual motion computations in mouse cortex Nature Neuroscience, 2017

A Wertz, S Trenholm, K Yonehara, D Hillier, Z Raics, M Leinweber, G Szalay, A Ghanem, G Keller, B Rozsa, K Conzelmann, B Roska: Single-cell-initiated monosynaptic tracing reveals layer-specific cortical network modules Science, Vol 349, Issue 6243 pp. 70-74, 2015

T Szikra, S Trenholm, A Drinnenberg, J Juttner, Z Raics, K Farrow, M Biel, G Awatramani, D Clark, J Sahel, R da Silveira, B Roska: Rods in daylight act as relay cells for cone-driven horizontal cell-mediated surround inhibition Nature Neuroscience, 2014

CARRIER

Measurement Automation Software Developer

 

At SENS Software LLC we are developing Python based measurement automation solutions for neurobiology research. Do you want to contribute to pioneering science and clinical research? Do you have the engineer’s mindset and interested in how software can drive real-world devices? This opportunity is for you:

Your Responsibilities

  • Develop, maintain and deploy software controlling scientific experiments, build prototypes of experimental setups
  • Write elegant and maintainable code for our measurement automation software framework
  • Participate in establishing analysis solutions for microscopy and electrophysiology data.

Your Profile

  • BS/MS degree in electrical engineering or computer science
  • 3+ years experience in two of Python/C++/Matlab
  • Familiar with electronics and measurement automation systems
  • Ability to develop software in remote environments
  • Fluent in English
  • Action-oriented, problem-solving, results-driven and able to work independently.
  • Experience with some of the following topics is also a plus:
    • NI data acquisition board and driver programming
    • QT based GUI development
    • Microcontroller programming

We Offer

  • Salary is based on your experience level

  • Flexible worktime
  • Bird whistle in office, silent relaxed working environment

  • Onboarding training

  • Hobby projects to develop your own ideas

  • Accommodation available if needed

We are located in Debrecen, Hungary, this is a full time job, home office up to 60%.

Further information: +36 30 6885376

Send application to Zoltan Raics to zoltan.raics@sens.hu.

 

CONTACT