CHALLENGE A
Predict the spike timing of a regular spiking L5 pyramidal cell responding to in-vivo-like current injection.
Experimental Methods
The experiments were performed by Thomas Berger and Richard Naud in the laboratory of Henry Markram at the EPFL. A 14-day-old Wistar rat was decapitated and its brain was quickly transferred to a slicing chamber filled with iced artificial cerebrospinal fluid (ACSF). 300 mm thick slices of the primary somatosensory neocortex were prepared using a HR2 vibratome (Sigmann Elektronik, Heidelberg, Germany). Slices were incubated at 36◦C for 45 min and left at room temperature until recording. The ACSF contained (in mM): 125 NaCl, 2.5 KCl, 25 D-glucose, 25 NaHCO3 , 1.25 NaH2PO4, 2 CaCl2, and 1 MgCl2 .
Somatic recordings were performed at 33-35◦C with a Axopatch 200B amplifier (Molecular Devices, Union City, CA) in the current clamp mode. Voltage traces were filtered with a 2.4 kHz Bessel filter. The amplifier was connected to a ITC-18 acquisition board (Instrutech Co, Port Washington, NY), which was in turn connected to a PC or Macintosh running a custom written routine under IgorPro (Wavemetrics, Portland, OR). Patch pipettes were pulled with a Flamming/Brown micropipette puller P-97 (Sutter Instruments Co, Novato, CA) and had an initial resistance of < 4MΩ. Pipettes were filled with intracellular solution (ICS) containing (in mM): 110 potassium gluconate, 10 KCl, 4 ATP-Mg, 10 Na-Phosphocreatine, 0 3 Na-GTP,10 Hepes, 30 Mannitol, and 8 Biocytin. Chemicals were provided by SIGMA or MERCK. The liquid junction potential between the ACSF and the ICS was around 12 mV and not corrected for.
The current-clamp stimulus has two parts. The first part is 17.5 seconds of various stimulus waveforms frequently used to calibrate neuron models. It consists of a series of four step current with a duration of 2 seconds and an inter-step rest time of two seconds (one hyperpolarizing and 3 depolarizing steps). The steps are followed by an injection of white noise of two seconds. The white noise injection can be used to remove the artefact introduced by the electrode while recording the voltage (Brette et al 2008, Badel et al 2008). The second part of the stimulus takes the remaining 42.5 seconds and is made of a simulated excitatory and inhibitory spike train. Six spike train were simulated as inhomogeneous poisson processes with predefined intensity as a function of time. The first three were convolved with a mono-exponential decay of time constant of 2 ms while the last three spike trains were convolved with a mono-expontential decay of time constant of 10 ms. The six resulting time-series were then combined into a single time-series by weighted sum. The weights were chosen such as to drive the neuron to a firing frequency between 5 and 10 Hz, as seen in experiments in vivo. The time-dependent intensity of the poisson process was consisted of a concatenation of blocks of 300-500 ms duration each having a constant intensity chosen randomly between 0 and 50 Hz. Both the amplitude and the duration of the blocks were drawn from a uniform distribution.
Evaluation Methods
Thirteen repetitions of the 60s-stimulation protocol specified above were injected while the voltage was measured at the same electrode. The training set consists of the first 38 s and the test set consist of the last 22 s. We provide the injected current waveform in pA for both training and test phases. For training the participants have access to the voltage trace of each repetition for the first 38 s. For testing, the participants must predict the spike times of the remaining 22 s, in each repetition.
Details on the quantitative aspects of the evaluation are available from the instructions.Submission
Submissions are made through this website. The participant must provide his prediction of spike times for each repetition. The submission consists of a folder containing 13 files, one for each repetition. Each file contains the predicted spike times in milliseconds (ms) since the beginning of the repetition. Spike times need to be stored as columns in ASCII file format. The files are labeled from 1 to 13 and are called ’repXX.txt’ (rep1.txt, ... rep13.txt). Submissions must comply with these specifications to ensure that the automatic evaluation of the results is successful.
