Deliverable M9-3: Workshop for definition of a detailed version of the V1 hypercolumn model

The INCM was holding a workshop on the V1 hypercolumn model on the 22nd and 23rd of October 2007. The purpose of the workshop was to promote the coordination of modeling efforts within the consortium and in particular to organize collaboration in WP9T2 and associated work-packages. It is labeled as deliverable M9-3: "Workshop for definition of a detailed version of the V1 hyper-column model" for WP9-2 (workpackage 9 task 2), but is also linked by its subject to WP5. In contrast to the previous meeting, we started with brief presentations of the results from each group to expose the different efficient aspects of each model. This allowed us in the second half of the workshop to converge to some main issues and prioritize the neural features that are the most important for the efficiency of V1. As for the format, we proposed that PhD students and post-docs should have the opportunity to present this work to give them experience and reduce the burden on busy chiefs. We felt it was important to involve as many in this workshop as possible as we approach a crucial stage in integrating the different models.


Afternoon of Monday, 22 October 07: Framework


Registration and Lunch

14:00-18:00 (First session)

Introduction: coordination of modeling efforts for WP9T2


Guillaume Masson (INCM): Welcome


  • Laurent presented some examples of using the benchmark structure proposed in NeuroTools and the new SpikeList object. The benchmark will be the privileged way of spreading the different benchmarks to all partners and is a practical way of describing a benchmark as a list of experiments, storing the result of the experiments, distribute and run the experiments on a cluster and finally for plotting figures. In a second part, Laurent presented the SpikeList object as an answer to the difficulty of finding a common format for describing lists of spikes. Some experimental example and an interface with PyNN was shown as a proof of concept. Jan suggested that the internal representation could be sparse. This should be easily done by using the format methods (See SpikeList).


  • Andrew and Jens presented a system's approach to modeling the visual system. Partners in FACETS need to exchange knowledge on their modeling progress and this approach allowed to construct a model from composite parts (retina, LGN, V1) from the “LEGO bricks” of the different groups. A practical example with INRIA/INCM retina and a INCM V1-layer 4 was shown. An LGN brick is to be developed. Brick for higher areas (MT) can also be developed.




  • Andrew proposed a format specification for benchmarks : 1) the input is provided as zipped PNG files, storing is done in the FACETS knowledge base (every stimulus has a unique URL), 2) A specification scheme for writing benchmarks and a whole experiment was presented with a proposed format using a XML interface.


  • Adrien presented his physiologically realistic retina, emphasizing on the contrast gain control. His model uses the INRIA simulator but with an open architecture and specification compatible with the FACETS specification. The retina uses a feed-back on the bipolar cells to achieve realistic contrast gain control which was compared with classical experiments (Shapley and Victor, 79, Enroth and Cugell XX). A possible extent is to study the importance of the spike profile at image onset which reveals first the luminance image and then the edges (Enroth Cugell 83 Bernadete-Kaplan 99). He also approached a mean field approach valid for gratings.


  • Klaus presented the retina used at the TUG. It is based on a spatio-temporal decorrelation model from Dong and Attick (1995) for the linear part and on a gamma renewal process (Gazères, 1998) for the spiking part. It is available to FACETS partners in the SVN1 and will converted to the format specified in the VisualSytem class (See ).


General Discussion

  • conclusions on benchmarking progress and decisions about their future development and use.

  • We concluded on benchmarking progress and decided about their future development and use. In particular, the unification proposed by the Benchmark class and the SpikeList object from Laurent and the specification proposed by Andrew seemed to fit to the needs of the partners and we agreed to use the proposed schemes.

  • We agreed on further definition of the visual benchmarks WP9T2-VisionBenchmarks (while respecting the standards from FACETS_Benchmarks). This will be implemented in a coming deliverable.

  • The question if we can reach the goal a single, common framework for multiple V1 models in FACETS was left open due to the wide variety of approaches in the consortium. However, the discussion suggested some collaborations of groups on some specific scientific questions.

Morning of Tuesday, 23rd of october 07

09:00-13:00 (Second session)

Progress in Modeling V1

  • 09:00-09:20*

  • Mike described current progress towards a neural model of motion perception in V1/MT, a collaborative project with CNRS/INCM. The model is based on the recurrent neural circuitry between a V1 hypercolumn and area MT, and uses a Kalman-Bucy approach to estimate the velocity of the moving object by integration of local motion information. The model will be suitable for testing using the FACETS visual motion benchmark stimuli, in particular the CNRS/INCM data on motion integration for smooth eye pursuit.*


  • The KTH model was presented by Jan, with the latest changes and additions and some preliminary results. HH neuronal models, hierarchical columnar structure. The horizontal connectivity is specified by the LISSOM model while the vertical connectivity is inspired by biology.*


  • Klaus presented the TUG model with the latest changes and some preliminary results. He illustrated the use of Izhikievitch neurons, the data from Alex Thomson (and not from Binzegger) by showing some results of the columnar model in particular by studying the influence of NMDA.*


  • Jens presented progress of the INCM/ALUF cooperation emphasizing on progress in the specification of the thalamo-cortical projections. He presented results of applying the different benchmarks proposed to reveal the functional properties of the model. It emerged that the inhibition scheme used allowed a normalization of the input at the network level. This was put into evidence using the spike-triggered conductance profile which were consistent with some recent data from Rudolph et al. (2007).*




  • Round-table discussion: questions, problems, and issues of modeling V1. Moderator: G. Masson

  • Retina model: shouldn't we use a more standardized input? How should we set up background noise? Biologists need to specify what they intend by background (on-going) activity to be simulated in large scale neural networks.

  • Back to back cooperation between experimentalists and modelers for defining benchmarks in connections with dissemination of experimental data.

  • Link with more high-level task, as the one presented by Mike and in WP9T3 or the work done in collaboration INCM-INRIA. Since they use the same benchmarks (such as motion integration), these approaches can better defined the computational rules to be implemented in large scale neural networks. One good example in the role of asymmetric diffusion of information/activity in the network, thanks to feedback from higher areas.



Afternoon of Tuesday, 23rd of october 07

14:00-16:30 (Third session)

Scientific questions coming from the Biology of V1


  • Julian presented a review of different results on the physiology and anatomy of the cat retino-thalamo-cortical projections. In fact, though the question of the architecture of these projections was questioned during the workshop, little is known with general agreement. Correlating different works from the literature, a detailed quantification was reviewed suggesting a disagreement between anatomy and physiology. Presenting the work of Ringach (2004), he concluded by showing own simulations suggesting that the properties and diversity of the receptive field of cat's area 17 simple cells may be captured by a wiring scheme based on the specific quantization of the parameters of the retino-thalamo-cortical pathway.*


  • Cyril reviewed different models of the emergence of orientation and direction selectivity before emphasizing on the results of different groups on the role of conductance profile in this function. This revealed a diversity of behavior between push-pull model where inhibitory and excitatory profiles are in overlap and other configuration This was put in light with results obtained at the UNIC.*


  • Alex presented preliminary results of center-surround interactions using VSD optical imaging in the primate V1 cortex. In the retinotopic position of the center the response to the center appears with decreasing latency for increasing contrast. The response of the 80% contrast surround reaches the center at a latency equivalent to approx. 15% contrast, leaving open the question of the interaction of these two information streams. Preliminary results show suppression for high contrasts but facilitation for low center contrast. Further analysis (of latency, propagation) suggests the functional role of horizontal propagation in this configuration.*




General Discussion Moderator: Yves Fregnac (UNIC)


Outcome: Planning of Implementation plans / priorities for WP9T2.

  • Several actions need to be taken. 1) We keep the idea of one annual meeting on V1 modeling. The meeting shall be held in June instead of October, to prepare for Annual reports and implementation plan. We will post a call for the organization of the 2008 meeting. We should also try to bring more biologists in these meetings. 2) We will organize a phone/video conference once every 3 months to exchange information and compare outputs for each benchmark steps. 3) We shall provide a timeline for delivering benchmark tools and objectives, as well as deadline for collecting results for testing models. Such a timeline will be added to the D9-2 in which we will describe the different benchmarks. 4) We will set a discussion list on the FACETS Wiki website to propose new questions from modelers to biologist and vice-versa. The idea is to put information for which there is a general agreement rather than having an on-going forum. Answers shall be concise, with reference to published work and or available data. 5) We shall promote active collaboration between sites with the objectives of common publication of one specific aspects of visual tasks to be develop in FACETS (on-going activity, local cortical point spread function ….)


Below are some questions modelers (please add to this list) would like the biologists at the meeting to answer during the round-table discussion (11:30-13:30 on 23 October):

  • What is the purpose of the Y-type pathway input to layer 4 of cat area 17?

  • Is the tuning of cortical neurons dynamic or not (e.g. for orientation)?

  • Can simple or complex cortical cells be directionally selective but untuned for orientation?

  • Are inhibitory neurons in cortex generally tuned for orientation or not?

  • Do inhibitory fast-spiking (FS) neurons have a higher spiking threshold than excitatory regular-spiking (RS) neurons?

  • Is modelling corticothalamic feedback essential for models of V1?

  • What common mistakes do modellers make that annoy you and fellow biologists the most?

  • How can modellers best help the biologists?

For the sake of fairness, we would also like some questions from the biologists for modellers to answer during the same discussion session.


When and where?

The date for the workshop is Monday, 22 and Tuesday, 23 October 07. It will take place at the INCM in Marseille as last meeting (see Marseille_November2006 ).

Who is attending

Please register your attendance.

  • monday lunch 16 people (everybody except Anders Lansner)

  • monday dinner 15 people (everybody except Anders Lansner and Andrew Davison)

  • tuesday lunch 16 people (everybody except Andrew Davison)


we will have

  • a beamer

  • no internet connection (ask if you need one)

  • lunch and coffee breaks!

  • ( the video conferencing system was not needed anymore)

more info