CHALLENGE C
Experimental Methods
The experiments were performed by Brice Bathellier and Richard Naud in the lab of Matthew Larkum at the university of Bern. Parasagittal brain slices of the somato-sensory cortex (300-350 m thick ) were prepared from 28-35 days-old Wistar rats. Slices were cut in ice-cold extracellular solution (ACSF), incubated at 34◦C for 20 min and stored at room temperature. During experiments, slices were superfused with in ACSF at 34◦C. The ACSF contained (in mM) 125 NaCl, 25 NaHCO3, 25 Glucose, 3 KCl, 1.25 NaH2PO4, 2 CaCl2 , 1 MgCl2 , pH 7.4, and was continuously bubbled with 5 % CO2 / 95 % O2. The intracellular solution contained (in mM) 115 K+-gluconate, 20 KCl, 2 Mg-ATP, 2 Na2-ATP, 10 Na2-phosphocreatine, 0.3 GTP, 10 HEPES, 0.1, 0.01 Alexa 594 and biocytin (0.2%), pH 7.2.
Recording electrodes were pulled from thick-walled (0.25 mm) borosilicate glass capillaries and used without further modification (pipette tip resistance 5-10 MΩ for soma and 20-30MΩ for dendrites). Whole-cell voltage recordings were performed at the soma of layer V pyramidal cells . After opening of the cellular membrane a fluorescent dye, Alexa 594 could diffuse in the entire neuron allowing to perform patch clamp recordings on the apical dendrite 600-700 μm from the soma. Both recordings were obtained using Axoclamp Dagan BVC-700A amplifiers (Dagan Corporation). Data was acquired with an ITC-16 board (Instrutech) at 10 kHz driven by routines written in the Igor software (Wavemetrics).
The injection waveform consisted of 6 blocks of 12 seconds. Each block is made of three parts: 1) one second of low-variance colored noise injected only in the soma, 2) one second of low-variance colored noise injected only in the dendritic injection site, 3) ten seconds of high-variance colored noise whose injection site depends on the block: In the first block, the 10-second stimulus is injected only in the dendritic site, the second block delivers a the 10-second stimulus in the soma only, and the four remaining blocks deliver simultaneous injection in the soma and the dendrites. The colored noise was simulated with MATLAB as an Ornstein-Uhlenbeck process with a correlation time of 3 ms. The six blocks make a 72 seconds stimulus that was injected repeatedly without redrawing the colored noise (frozen-noise). Twenty repetitions of the 72-second stimulus were carried out, separated by periods of 2-120 seconds. Out of the twenty repetitions, a set of seven successive repetitions were selected on the basis of high intrinsic reliability (see “Evaluation Methods”).
Evaluation Methods
Seven repetitions of a current waveform of 72 seconds were injected in dendritic and somatic injection site while the voltage was measured with the same electrodes. The training set consists of the first 38 s and the test set consists of the last 34 s. We provide the somatic and dendritic current waveform in pA for both training and test phases. For training the participants have access to the voltage trace of each repetition in each recording site for the first 38 s. For testing, the participants must predict the somatic spike times of the remaining 34 s, in each repetition. The complementary evaluation methods are identical to those described for challenge A.
Submission
Submissions are made through this web. The participant must provide his prediction of spike times for each repetition. The submission consists of a folder containing 7 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 7 and are called ’repXX.txt’ (rep1.txt, ... rep7.txt). Submissions must comply with these specifications to ensure that the automatic evaluation of the results is successful.
