OSCR

Representations of the intrinsic value of information in mouse orbitofrontal cortex.

Code ↔ Paper

21 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 21 matches · 1 of them tie a paragraph to a whole file, not to given lines: a weak match, whose lines are not tinted
  1. [1] § Methods › Imaging data processing ↔ 03 ImagingCellExtractionPipeline/CNMFE_pipe.m, lines 37–148 · score 0.99 · gSig, gSiz, min_corr_res, min_pnr_res, min_pixel, minimum peak
  2. [2] § Methods › Imaging data processing ↔ 04 ImagingAnalysis/CellRegistrationMulti.m, lines 95–141 · score 0.92 · CaImAn, options.dist_maxthr, options.dist_thr, register_multisession, Cell registration, rois
  3. [3] § Methods › Imaging data processing ↔ 03 ImagingCellExtractionPipeline/CNMFE_pipe.m, lines 37–148 · score 0.89 · background fluctuation, spatially downsampled, motion corrected, Gaussians, smaller, filtered
  4. [4] § Methods › Analysis of neural activity ↔ 01 Bpod/InfoseekWaterVal/InfoseekWaterVal.m, lines 73–120 · score 0.81 · valve opening, odor onset, odor valves, Bpod system, side port odor, center port odor
  5. [5] § Methods › Analysis of neural activity ↔ 01 Bpod/InfoseekSyncSignal2/InfoseekSyncSignal2.m, lines 54–104 · score 0.81 · valve opening, odor onset, odor valves, Bpod system, side port odor, center port odor
  6. [6] § Methods › Behavior training and testing › Main task ↔ 01 Bpod/InfoseekWaterVal/InfoseekWaterVal.m, lines 2–59 · score 0.78 · mineral oil, Latch valves, Bpod system, olfactometers, modules, side port
  7. [7] § Methods › Imaging data processing ↔ 04 ImagingAnalysis/CellRegistrationMulti.m, lines 95–141 · score 0.78 · bin_width, max_shift, iter, NormCorre, template, CNMF
  8. [8] § Results › Mice value information ↔ 02 BehaviorAnalysis/InfoseekBehaviorModel_Finalized_CV.m, lines 373–425 · score 0.77 · delay discounted, lose shift, RLinfo, RLwater, win stay, exponential
  9. [9] § Methods › Behavior training and testing › Main task ↔ 01 Bpod/InfoseekSyncToneGo/InfoseekSyncToneGo.m, lines 1–50 · score 0.75 · alternative forced choice, reward outcome, amplifier, speaker, hardware, module
  10. [10] § Methods › Behavior training and testing › Main task ↔ 01 Bpod/InfoseekWaterVal/InfoseekWaterVal.m, lines 2–59 · score 0.72 · HiFi, forced choice, sound, hardware, water reward, module
  11. [11] § Methods › Behavior training and testing › Main task ↔ 01 Bpod/InfoseekSyncSignal2/InfoseekSyncSignal2.m, lines 970–1007 · score 0.71 · Lee Company, Latch valves, Bpod system, modules, ports, odors
  12. [12] § Methods › Behavior training and testing › Main task ↔ 01 Bpod/InfoseekWaterVal/InfoseekWaterVal.m, lines 73–120 · score 0.70 · grace period, go cue, side port odor, correct side port, poking, center odor
  13. [13] § Methods › Behavioral models ↔ Functions/fitPsyche.m, lines 1–42 · score 0.61 · psychometric curve, fitPsycheCurveWH, fitting, model
  14. [14] § Methods › Behavior analysis ↔ 02 BehaviorAnalysis/BehaviorAnalysisAll.m, lines 1075–1168 · score 0.61 · choice preference, glmfit, binomial, logit, binofit, signrank
  15. [15] § Methods › Behavioral models ↔ 02 BehaviorAnalysis/InfoseekBehaviorModel_Finalized_CV.m, lines 373–425 · score 0.61 · win stay lose, shift, model, weighted, Behavioral, reward
  16. [16] § Methods › Behavior training and testing › Water and delay titration experiments ↔ 02 BehaviorAnalysis/InfoseekBehaviorModel_Finalized_CV.m, lines 122–218 · score 0.57 · delay titration, reward amount, water reward, reverse, preference, modeling
  17. [17] § Methods › Analysis of neural activity ↔ Functions/absolute_rocarea.m, the whole file · a weak match · score 0.56 · vice versa, halves, split, odd
  18. [18] § Methods › CEBRA modeling ↔ 04 ImagingAnalysis/InfoseekNeuralAnalysisLearning.m, lines 33–109 · score 0.56 · long delay, JB433, JB424, JB434, JB425, JB426
  19. [19] § Methods › Behavioral models ↔ 02 BehaviorAnalysis/InfoseekBehaviorModel_Finalized_CV.m, lines 122–218 · score 0.54 · negative log likelihood, minimization, Behavioral, models
  20. [20] § Methods › Behavior training and testing › Behavioral training ↔ 01 Bpod/InfoseekSyncSignal2/InfoseekSyncSignal2.m, lines 54–104 · score 0.53 · center poke, center port odor, side port, duration, interval, Delivery
  21. [21] § Methods › Cells with significant conditional responses to task events (responding cells) ↔ 04 ImagingAnalysis/InfoseekNeuralAnalysis.m, lines 485–546 · score 0.52 · exponential decay, responding, baseline, post, event, pre

Paper

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The authors' code

MATLAB · 1,278 lines · 56 KB · no license · 4 matches

  2. %{
  3. ----------------------------------------------------------------------------
  4. InfoseekWaterVal — Protocol for task with 4 center ports odors to compare information and water value
  5. ----------------------------------------------------------------------------
  7. Runs four forced-choice trial types cued by odor at the center port: information, no information (random),
  8. high water value (big), low water value (small). Usually, the same side (left/right) is assigned to information
  9. and small.
  11. TASK STRUCTURE (per trial):
  12. 1. Mouse pokes center port → receives an odor cueing the forced side
  13. for this trial (info, rand, big, small)
  14. 2. Mouse pokes the cued side port
  15. 3. Side port delivers a second odor (only on information or random trials)
  16. 4. After a delay (with an auditory warning tone predicting reward size),
  17. water reward is delivered at the same port
  18. (mouse must be present in port only at outcome time to receive reward)
  20. TRIAL TYPES (set by S.GUI.TrialTypes):
  21. 1 = Small — center odor = SmallOdor
  22. 2 = Info Forced — center odor = InfoOdor
  23. 3 = Rand Forced — center odor = RandOdor
  24. 4 = Big — center odor = BigOdor
  26. SIDE ASSIGNMENT:
  27. S.GUI.InfoSide (0/1): 0 = Info odors (A/B) go LEFT, Rand odors (C/D) go RIGHT
  28. 1 = Info odors (A/B) go RIGHT, Rand odors (C/D) go LEFT
  29. S.GUI.BigSide (0/1): 0 = Big water trials go LEFT, Small water trials go RIGHT
  30. 1 = Big water trials go RIGHT, Small water trials go LEFT
  31. Info and small water normally set to the same side.
  33. HARDWARE:
  34. ValveModule1 — control mineral oil (center / left / right)
  35. ValveModule2/3 — odor valves (8 positions each)
  36. DIOmodule (Teensy) — buzzer, latch valves (flip side port odors from left to right)
  37. HiFi module (H) — go-cue tone and reward-predictive tones (sounds 1-3 loaded at start)
  38. BNC1/2 — sync signals to DAQ/miniscope/tracking camera via GlobalTimers 7/8
  40. REWARD DROPS:
  41. Drops are delivered via looping GlobalTimers (3 = left valve, 4 = right).
  42. Drop counts controlled by S.GUI.Info/Rand Big/SmallDrops and S.GUI.Big/SmallDrops.
  44. OUTCOME CODES (BpodSystem.Data.Outcomes):
  45. 1 = Small no-choice 5 = Info no-choice 11 = Rand no-choice 17 = Big no-choice
  46. 2 = Small correct 6 = Info big 12 = Rand big 18 = Big correct
  47. 3 = Small NP 7 = Info big NP 13 = Rand big NP 19 = Big NP
  48. 4 = Small incorrect 8 = Info small 14 = Rand small 20 = Big incorrect
  49. 9 = Info small NP 15 = Rand small NP
  50. 10 = Info incorrect 16 = Rand incorrect
  51. ----------------------------------------------------------------------------
  53. Three valve control modules control airflow in the custom dilution
  54. olfactometer.
  56. One Teensy 3.2 connected as a module with the Bpod Teensy Shield controls
  57. a buzzer (not used when Hifi tones in use) and latch valves via 2 H-bridges.
  59. %}
  60. function InfoseekWaterVal
  62. global BpodSystem
  64. %% Assert HiFi module is present + USB-paired (via USB button on console GUI)
  65. BpodSystem.assertModule('HiFi', 1); % The second argument (1) indicates that the HiFi module must be paired with its USB serial port
  67. % Create an instance of the HiFi module
  68. H = BpodHiFi(BpodSystem.ModuleUSB.HiFi1); % The argument is the name of the HiFi module's USB serial port (e.g. COM3)
  70. %% Create trial manager object
  71. TrialManager = TrialManagerObject;
  73. %% Define parameters
  75. S = BpodSystem.ProtocolSettings; % Load settings chosen in launch manager into current workspace as a struct called S
  76. if isempty(fieldnames(S)) % No saved settings — populate with defaults
  77. % Session structure
  78. S.GUI.SessionTrials = 1000;
  79. S.GUI.TrialTypes = 2; % 1=Small, 2=Info, 3=Rand, 4=Big, 5-8=mixes (see SetTrialTypes)
  80. S.GUI.InfoSide = 0; % 0=info→left/rand→right, 1=info→right/rand→left
  81. S.GUI.BigSide = 0; % 0=big→left/small→right, 1=big→right/small→left
  83. % Center-port odor valve indices (positions on ValveModule2/3)
  84. S.GUI.InfoOdor = 2;
  85. S.GUI.RandOdor = 0;
  86. S.GUI.BigOdor = 3;
  87. S.GUI.SmallOdor = 1;
  89. % Side-port odor valve indices
  90. S.GUI.OdorA = 3; % Info big
  91. S.GUI.OdorB = 2; % Info small
  92. S.GUI.OdorC = 0; % Rand big
  93. S.GUI.OdorD = 1; % Rand small
  95. % Timing (seconds)
  96. S.GUI.CenterDelay = 0; % delay after center poke before odor onset
  97. S.GUI.CenterOdorTime = 0.2; % duration of center-port odor (s)
  98. S.GUI.StartDelay = 0; % delay after center odor before go cue
  99. S.GUI.OdorDelay = 0; % delay after go cue before side odor onset
  100. S.GUI.OdorTime = 0; % duration of side-port odor (s)
  101. S.GUI.RewardDelay = 0.5; % delay from odor offset to reward delivery (s)
  102. S.GUI.Signal = 0.2; % fraction of RewardDelay spent as an audible/light warning before reward
  103. S.GUI.GracePeriod = 100000000; % additional time (s) to wait for response after go cue on top of OdorDelay; odor then delivered immediately upon correct side port entry
  104. S.GUI.Interval = 1; % inter-trial interval (s)
  106. % Reward drops (number of valve open/close cycles per reward)
  107. S.GUI.InfoBigDrops = 1;
  108. S.GUI.InfoSmallDrops = 1;
  109. S.GUI.RandBigDrops = 1;
  110. S.GUI.RandSmallDrops = 1;
  111. S.GUI.BigDrops = 8;
  112. S.GUI.SmallDrops = 2;
  114. % Reward probability (fraction of trials that give big reward; rest give small)
  115. S.GUI.InfoRewardProb = 1;
  116. S.GUI.RandRewardProb = 1;
  118. BpodSystem.ProtocolSettings = S;
  119. SaveProtocolSettings(BpodSystem.ProtocolSettings);
  120. end
  122. %% Set Latch Valves
  123. SetLatchValves(S);
  125. %% Set up trial types and rewards
  127. S.TrialTypes = [];
  128. S.RewardTypes = [];
  129. S.RandOdorTypes = [];
  130. S = SetTrialTypes(S,1); % Sets S.TrialTypes from trial 1 to maxTrials
  131. S = SetRewardTypes(S,1); % Sets S.RewardTypes, S.RandOdorTypes from trial 1 to maxTrials
  133. %% SET INITIAL TYPE COUNTS
  135. BpodSystem.Data.TrialCounts = [0,0,0,0];
  136. BpodSystem.Data.PlotOutcomes = [];
  138. %% SAVE EVENT NAMES AND NUMBER
  140. BpodSystem.Data.TrialTypes = []; % The trial type of each trial completed will be added here.
  141. BpodSystem.Data.Outcomes = [];
  143. BpodSystem.Data.OrigTrialTypes = S.TrialTypes; % take out if working?
  144. BpodSystem.Data.OrigRewardTypes = S.RewardTypes; % take out if working?
  145. BpodSystem.Data.EventNames = BpodSystem.StateMachineInfo.EventNames;
  146. SaveBpodSessionData;
  148. %% Initialize plots
  150. BpodSystem.ProtocolFigures.TrialTypePlotFig = figure('Position', [50 640 1000 250],'name','Trial Type','numbertitle','off', 'MenuBar', 'none');
  151. BpodSystem.GUIHandles.TrialTypePlot = axes('OuterPosition', [0 0 1 1]);
  152. TrialTypePlotInfoWater(BpodSystem.GUIHandles.TrialTypePlot,'init',S.TrialTypes,min([S.GUI.SessionTrials 40])); % trial choice types
  153. % EventsPlot('init', getStateColors(S.GUI.InfoSide)); % events within trial
  155. BpodSystem.ProtocolFigures.OutcomePlotFig = figure('Position', [50 100 600 400],'name','TrialOutcomes','numbertitle','off', 'MenuBar', 'none');
  156. BpodSystem.GUIHandles.OutcomePlot = axes('OuterPosition', [0 0 1 1]);
  157. InfoWaterOutcomesPlot(BpodSystem.GUIHandles.OutcomePlot,'init');
  159. BpodNotebook('init');
  160. InfoParameterGUI('init', S); % Initialize parameter GUI plugin
  161. TotalRewardDisplayInfo('init');
  163. %% INITIALIZE SERIAL MESSAGES / DIO
  165. ResetSerialMessages();
  167. buzzer1 = [254 1];
  168. buzzer2 = [253 1];
  170. modules = BpodSystem.Modules.Name;
  171. DIOmodule = [modules(strncmp('DIO',modules,3))];
  172. DIOmodule = DIOmodule{1};
  174. % Set serial messages for Teensy module to control box, communicate with
  175. % DAQ/miniscope
  176. LoadSerialMessages(DIOmodule, {buzzer1, buzzer2,...
  177. [22 1],[22 0],[23 1], [23 0]});
  179. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  180. % ODOR CONTROL SERIAL MESSAGES
  181. LoadSerialMessages('ValveModule1',{[1 2],[3 4],[5 6]}); % control by port
  184. %% Define sounds and send to sound module
  185. sf = 192000; % Use max supported sampling rate
  186. H.SamplingRate = sf;
  188. noRewardFreq=500;
  189. rewardFreq=2000;
  190. toneDuration=0.5;
  192. rewardSound = GenerateSineWave(sf, noRewardFreq, toneDuration)*.9;
  193. % Sampling freq (hz), Sine frequency (hz), duration (s)
  194. noRewardSound = GenerateSineWave(sf, rewardFreq, toneDuration)*.9;
  196. goSound = GenerateSineWave(sf, 1200, 0.05)*.9;
  198. % Setup HiFi module
  199. % H.HeadphoneAmpEnabled = true; H.HeadphoneAmpGain = 10; % Ignored if using HD version of the HiFi module
  200. H.DigitalAttenuation_dB = -50; % Set a negative value here if necessary for digital volume control.
  201. H.load(1, rewardSound);
  202. H.load(2, noRewardSound);
  203. H.load(3, goSound);
  206. % Define 1ms linear ramp envelope of amplitude coefficients, to apply at sound onset + in reverse at sound offset
  207. envelope = 1/(sf*0.001):1/(sf*0.001):1;
  208. H.AMenvelope = envelope;
  211. %% INITIALIZE STATE MACHINE
  213. [sma,S,nextRewardLeft,nextRewardRight] = PrepareStateMachine(S, 1, []); % Prepare state machine for trial 1 with empty "current events" variable
  215. TrialManager.startTrial(sma); % Sends & starts running first trial's state machine. A MATLAB timer object updates the
  216. % console UI, while code below proceeds in parallel.
  217. RewardLeft = nextRewardLeft; RewardRight = nextRewardRight;
  219. %% MAIN TRIAL LOOP
  221. for currentTrial = 1:S.GUI.SessionTrials
  222. currentS = S;
  223. currentTrialEvents = TrialManager.getCurrentEvents({'WaitForOdorLeft','WaitForOdorRight','NoChoice','Incorrect'}); % Hangs here until Bpod enters one of the listed trigger states, then returns current trial's states visited + events captured to this point
  224. if BpodSystem.Status.BeingUsed == 0
  225. TurnOffAllOdors();
  226. return; end % If user hit console "stop" button, end session
  227. [sma, S, nextRewardLeft,nextRewardRight] = PrepareStateMachine(S, currentTrial+1, currentTrialEvents); % Prepare next state machine.
  228. SendStateMachine(sma, 'RunASAP'); % send the next trial's state machine while the current trial is ongoing
  229. RawEvents = TrialManager.getTrialData; % Hangs here until trial is over, then retrieves full trial's raw data
  230. if BpodSystem.Status.BeingUsed == 0
  231. TurnOffAllOdors();
  232. return; end % If user hit console "stop" button, end session
  233. HandlePauseCondition; % Checks to see if the protocol is paused. If so, waits until user resumes.
  234. TrialManager.startTrial(); % Start processing the next trial's events
  235. if ~isempty(fieldnames(RawEvents)) % If trial data was returned from last trial, update plots and save data
  236. BpodSystem.Data = AddTrialEvents(BpodSystem.Data,RawEvents); % Computes trial events from raw data
  237. [rewardAmount,outcome] = UpdateOutcome(currentTrial,currentS,RewardLeft,RewardRight);
  238. BpodSystem.Data.TrialSettings(currentTrial) = currentS.GUI; % Adds the settings used for the current trial to the Data struct (to be saved after the trial ends)
  239. BpodSystem.Data.TrialTypes(currentTrial) = currentS.TrialTypes(currentTrial); % Adds the trial type of the current trial to data
  240. BpodSystem.Data.Outcomes(currentTrial) = outcome;
  241. BpodSystem.Data = BpodNotebook('sync', BpodSystem.Data); % Sync with Bpod notebook plugin
  242. TotalRewardDisplayInfo('add',rewardAmount);
  243. RewardLeft = nextRewardLeft; RewardRight = nextRewardRight;
  244. TrialTypePlotInfoWater(BpodSystem.GUIHandles.TrialTypePlot,'update',currentTrial,S.TrialTypes);
  245. InfoWaterOutcomesPlot(BpodSystem.GUIHandles.OutcomePlot,'update');
  246. tic
  247. SaveBpodSessionData;
  248. toc
  249. end
  251. end
  253. end % end of protocol main function
  256. %% PREPARE STATE MACHINE
  258. function [sma, S, RewardLeft, RewardRight] = PrepareStateMachine(S, nextTrial, currentTrialEvents)
  259. % Build state machine for nextTrial.
  260. % currentTrialEvents: events captured so far from the current (running) trial,
  261. % used to detect early port entry and extend trial type arrays if needed.
  262. % Returns updated S, and the reward valve timer counts for left/right.
  264. global BpodSystem;
  266. modules = BpodSystem.Modules.Name;
  267. DIOmodule = [modules(strncmp('DIO',modules,3))];
  268. DIOmodule = DIOmodule{1};
  270. lastS = S;
  271. S = InfoParameterGUI('sync', S); % Sync parameters with BpodParameterGUI plugin
  274. if S.GUI.TrialTypes ~= lastS.GUI.TrialTypes
  275. S = SetTrialTypes(S,nextTrial);
  276. end
  278. if (S.GUI.InfoRewardProb ~= lastS.GUI.InfoRewardProb || S.GUI.RandRewardProb ~= lastS.GUI.RandRewardProb)
  279. S = SetRewardTypes(S,nextTrial);
  280. end
  282. if (S.GUI.InfoSide ~= lastS.GUI.InfoSide)
  283. SetLatchValves(S);
  284. end
  286. % DETERMINE TRIAL TYPE
  287. if nextTrial>1
  288. previousStates = currentTrialEvents.StatesVisited;
  289. if sum(contains(previousStates,'NoChoice') | contains(previousStates,'Incorrect'))>0
  290. S = UpdateTrialTypes(nextTrial,S);
  291. end
  292. end
  294. nextTrialType = S.TrialTypes(nextTrial);
  296. infoSide = S.GUI.InfoSide;
  297. TrialCounts = BpodSystem.Data.TrialCounts;
  298. bigSide = S.GUI.BigSide;
  300. % Determine trial-specific state matrix fields
  301. % Set trialParams (reward and odor)
  302. switch nextTrialType
  303. case 1 % SMALL
  304. ThisCenterOdor = S.GUI.SmallOdor;
  305. LeftSideOdor = 0;
  306. RightSideOdor = 0;
  307. if bigSide == 0 % BIG LEFT
  308. ChooseLeft = 'Incorrect'; ChooseRight = 'WaitForOdorRight';
  309. RewardLeft = 0; RewardRight = 1;
  310. OutcomeStateLeft = 'TimeoutOutcome';
  311. LeftRewardDrops = 0;
  312. SideOdorStateLeft = 'TimeoutOdor';
  313. SideOdorStateRight = 'OdorWaterRight';
  314. SideOdorOffActionRight = [];
  315. SideOdorOffActionLeft = [];
  316. ToneCmd =[];
  317. OutcomeStateRight = 'RightSmallReward';
  318. RightRewardDrops = S.GUI.SmallDrops;
  319. else
  320. ChooseLeft = 'WaitForOdorLeft'; ChooseRight = 'Incorrect';
  321. RewardLeft = 1; RewardRight = 0;
  322. OutcomeStateRight = 'TimeoutOutcome';
  323. RightRewardDrops = 0;
  324. SideOdorStateRight = 'TimeoutOdor';
  325. SideOdorStateLeft = 'OdorWaterLeft';
  326. SideOdorOffActionRight = [];
  327. SideOdorOffActionLeft = [];
  328. ToneCmd =[];
  329. OutcomeStateLeft = 'LeftSmallReward';
  330. LeftRewardDrops = S.GUI.SmallDrops;
  331. end
  333. case 2 % INFO FORCED
  334. ThisCenterOdor = S.GUI.InfoOdor;
  335. if infoSide == 0
  336. % info on left
  337. RewardLeft = S.RewardTypes(TrialCounts(2)+1,1); RewardRight = 0;
  338. ChooseLeft = 'WaitForOdorLeft'; ChooseRight = 'Incorrect';
  339. RightSideOdor = 0;
  340. if RewardLeft == 1
  341. OutcomeStateLeft = 'LeftBigReward';
  342. LeftRewardDrops = S.GUI.InfoBigDrops;
  343. LeftSideOdor = S.GUI.OdorA;
  344. SideOdorStateLeft = 'OdorALeft';
  345. ToneCmd = {'HiFi1', ['P' 0]};
  346. else
  347. OutcomeStateLeft = 'LeftSmallReward';
  348. LeftRewardDrops = S.GUI.InfoSmallDrops;
  349. LeftSideOdor = S.GUI.OdorB;
  350. SideOdorStateLeft = 'OdorBLeft';
  351. ToneCmd = {'HiFi1', ['P' 1]};
  352. end
  353. SideOdorOffActionLeft = RunOdor(LeftSideOdor,1);
  354. SideOdorOffActionRight =[];
  355. OutcomeStateRight = 'TimeoutOutcome';
  356. RightRewardDrops = 0;
  357. SideOdorStateRight = 'TimeoutOdor';
  358. else
  359. RewardLeft = 0; RewardRight = S.RewardTypes(TrialCounts(2)+1,1);
  360. ChooseLeft = 'Incorrect'; ChooseRight = 'WaitForOdorRight';
  361. LeftSideOdor = 0;
  362. if RewardRight == 1
  363. OutcomeStateRight = 'RightBigReward';
  364. RightRewardDrops = S.GUI.InfoBigDrops;
  365. RightSideOdor = S.GUI.OdorA;
  366. SideOdorStateRight = 'OdorARight';
  367. ToneCmd = {'HiFi1', ['P' 0]};
  368. else
  369. OutcomeStateRight = 'RightSmallReward';
  370. RightRewardDrops = S.GUI.InfoSmallDrops;
  371. RightSideOdor = S.GUI.OdorB;
  372. SideOdorStateRight = 'OdorBRight';
  373. ToneCmd = {'HiFi1', ['P' 1]};
  374. end
  375. SideOdorOffActionRight = RunOdor(RightSideOdor,2);
  376. SideOdorOffActionLeft =[];
  377. OutcomeStateLeft = 'TimeoutOutcome';
  378. LeftRewardDrops = 0;
  379. SideOdorStateLeft = 'TimeoutOdor';
  380. end
  381. case 3 % RAND FORCED
  382. ThisCenterOdor = S.GUI.RandOdor;
  383. if infoSide == 0 % INFO ON LEFT
  384. RewardLeft = 0; RewardRight = S.RewardTypes(TrialCounts(3)+1,2);
  385. ChooseLeft = 'Incorrect'; ChooseRight = 'WaitForOdorRight';
  386. RightSideOdorFlag = S.RandOdorTypes(TrialCounts(3)+1,1);
  387. if RightSideOdorFlag == 0
  388. RightSideOdor = S.GUI.OdorC;
  389. SideOdorStateRight = 'OdorCRight';
  390. else
  391. RightSideOdor = S.GUI.OdorD;
  392. SideOdorStateRight = 'OdorDRight';
  393. end
  394. LeftSideOdor = 0;
  395. SideOdorOffActionRight = RunOdor(RightSideOdor,2);
  396. SideOdorOffActionLeft =[];
  397. if RewardRight == 1
  398. OutcomeStateRight = 'RightBigReward';
  399. RightRewardDrops = S.GUI.RandBigDrops;
  400. ToneCmd = {'HiFi1', ['P' 0]};
  401. else
  402. OutcomeStateRight = 'RightSmallReward';
  403. RightRewardDrops = S.GUI.RandSmallDrops;
  404. ToneCmd = {'HiFi1', ['P' 1]};
  405. end
  406. OutcomeStateLeft = 'TimeoutOutcome';
  407. LeftRewardDrops = 0;
  408. SideOdorStateLeft = 'TimeoutOdor';
  409. else
  410. RewardLeft = S.RewardTypes(TrialCounts(3)+1,2); RewardRight = 0;
  411. ChooseLeft = 'WaitForOdorLeft'; ChooseRight = 'Incorrect';
  412. LeftSideOdorFlag = S.RandOdorTypes(TrialCounts(3)+1,1);
  413. if LeftSideOdorFlag == 0
  414. LeftSideOdor = S.GUI.OdorC;
  415. SideOdorStateLeft = 'OdorCLeft';
  416. else
  417. LeftSideOdor = S.GUI.OdorD;
  418. SideOdorStateLeft = 'OdorDLeft';
  419. end
  420. RightSideOdor = 0;
  421. SideOdorOffActionLeft = RunOdor(LeftSideOdor,1);
  422. SideOdorOffActionRight =[];
  423. if RewardLeft == 1
  424. OutcomeStateLeft = 'LeftBigReward';
  425. LeftRewardDrops = S.GUI.RandBigDrops;
  426. ToneCmd = {'HiFi1', ['P' 0]};
  427. else
  428. OutcomeStateLeft = 'LeftSmallReward';
  429. LeftRewardDrops = S.GUI.RandSmallDrops;
  430. ToneCmd = {'HiFi1', ['P' 1]};
  431. end
  432. OutcomeStateRight = 'TimeoutOutcome';
  433. RightRewardDrops = 0;
  434. SideOdorStateRight = 'TimeoutOdor';
  435. end
  436. case 4 % BIG
  437. ThisCenterOdor = S.GUI.BigOdor;
  438. LeftSideOdor = 0;
  439. RightSideOdor = 0;
  440. if bigSide == 0 % BIG LEFT
  441. ChooseLeft = 'WaitForOdorLeft'; ChooseRight = 'Incorrect';
  442. RewardLeft = 1; RewardRight = 0;
  443. OutcomeStateRight = 'TimeoutOutcome';
  444. RightRewardDrops = 0;
  445. SideOdorStateRight = 'TimeoutOdor';
  446. SideOdorStateLeft = 'OdorWaterLeft';
  447. SideOdorOffActionLeft = [];
  448. SideOdorOffActionRight =[];
  449. ToneCmd =[];
  450. OutcomeStateLeft = 'LeftBigReward';
  451. LeftRewardDrops = S.GUI.BigDrops;
  452. else
  453. ChooseLeft = 'Incorrect'; ChooseRight = 'WaitForOdorRight';
  454. RewardLeft = 0; RewardRight = 1;
  455. OutcomeStateLeft = 'TimeoutOutcome';
  456. LeftRewardDrops = 0;
  457. SideOdorStateLeft = 'TimeoutOdor';
  458. SideOdorStateRight = 'OdorWaterRight';
  459. SideOdorOffActionRight = [];
  460. SideOdorOffActionLeft =[];
  461. ToneCmd =[];
  462. OutcomeStateRight = 'RightBigReward';
  463. RightRewardDrops = S.GUI.BigDrops;
  464. end
  465. end
  467. % Water parameters
  468. R = GetValveTimes(4, [1 3]);
  469. % R = [0.100 0.100];
  470. LeftValveTime = R(1); RightValveTime = R(2); % Update reward amounts
  471. MaxValveTime = max(R);
  472. maxDrops = max([S.GUI.InfoBigDrops,S.GUI.InfoSmallDrops,S.GUI.RandBigDrops,S.GUI.RandSmallDrops,S.GUI.SmallDrops,S.GUI.BigDrops]);
  473. RewardPauseTime = 0.05;
  475. % Time for reward lights
  476. WarningTime = ceil(S.GUI.Signal*S.GUI.RewardDelay);
  477. DelayTime = S.GUI.RewardDelay - WarningTime;
  479. sma = NewStateMatrix(); % Assemble state matrix
  481. sma = SetCondition(sma, 1, 'Port1', 1); % Condition 1: Port 1 high (is in) (left)
  482. sma = SetCondition(sma, 2, 'Port2', 1); % Condition 2: Port 2 high (is in) (center)
  483. sma = SetCondition(sma, 3, 'Port3', 1); % Condition 3: Port 3 high (is in) (right)
  484. sma = SetCondition(sma, 4, 'Port1', 0); % Condition 4: Port 1 low (is out) (left)
  485. sma = SetCondition(sma, 5, 'Port2', 0); % Condition 5: Port 2 low (is out) (center)
  486. sma = SetCondition(sma, 6, 'Port3', 0); % Condition 6: Port 3 low (is out) (right)
  488. % TIMERS
  489. sma = SetCondition(sma, 7, 'GlobalTimer1', 0);
  491. % sma = SetGlobalTimer(sma, 'TimerID', 1, 'Duration', S.GUI.OdorDelay+0.05); % ODOR DELAY + GO CUE
  492. sma = SetGlobalTimer(sma, 'TimerID', 1, 'Duration', S.GUI.OdorDelay+0.05,...
  493. 'OnsetDelay', 0, 'Channel', 'SoftCode', 'OnMessage', 0, 'OffMessage', 0,...
  494. 'Loop', 0, 'SendEvents', 1, 'LoopInterval', 0,'OnsetTrigger','010000'); %also turn on timer 5
  496. % TIMER 2 FOR MAX REWARD
  497. if maxDrops > 1
  498. sma = SetGlobalTimer(sma, 'TimerID', 2, 'Duration', MaxValveTime,...
  499. 'OnsetDelay', 0, 'Channel', 'SoftCode', 'OnMessage',0, 'OffMessage', 0,...
  500. 'Loop', maxDrops, 'SendEvents', 1, 'LoopInterval', RewardPauseTime); % timer to stay in reward state
  501. else
  502. sma = SetGlobalTimer(sma, 'TimerID', 2, 'Duration', MaxValveTime,...
  503. 'OnsetDelay', 0, 'Channel', 'SoftCode', 'OnMessage', 0, 'OffMessage', 0,...
  504. 'Loop', 0, 'SendEvents', 1, 'LoopInterval', 0); % timer to stay in reward state
  505. end
  506. sma = SetGlobalCounter(sma, 2, 'GlobalTimer2_End', maxDrops);
  508. % reward states all wait for timers to end
  509. % set multiple timers for each outcome--one for drops, one for blanks
  510. % get rid of reward states
  512. % Timers for delivering reward drops
  513. if LeftRewardDrops > 1
  514. sma = SetGlobalTimer(sma,'TimerID',3,'Duration',LeftValveTime,'OnsetDelay',0,...
  515. 'Channel', 'Valve1', 'OnMessage', 1, 'OffMessage', 0, 'Loop',...
  516. LeftRewardDrops, 'SendEvents', 1, 'LoopInterval', RewardPauseTime,'OnsetTrigger', '10');
  517. sma = SetGlobalCounter(sma, 3, 'GlobalTimer3_End', LeftRewardDrops);
  518. elseif LeftRewardDrops == 1
  519. sma = SetGlobalTimer(sma,'TimerID',3,'Duration',LeftValveTime,'OnsetDelay',0,...
  520. 'Channel','Valve1','OnMessage', 1, 'OffMessage', 0, 'Loop', 0, 'SendEvents', 1,'LoopInterval',0,'OnsetTrigger', '10');
  521. sma = SetGlobalCounter(sma, 3, 'GlobalTimer3_End', 1);
  522. else
  523. sma = SetGlobalTimer(sma,'TimerID',3,'Duration',0,'OnsetDelay',0,...
  524. 'Channel','Valve1','OnMessage', 0, 'OffMessage', 0, 'Loop', 0, 'SendEvents', 1,'LoopInterval',0,'OnsetTrigger', '10');
  525. sma = SetGlobalCounter(sma, 3, 'GlobalTimer3_End', 1);
  526. end
  528. if RightRewardDrops > 1
  529. sma = SetGlobalTimer(sma,'TimerID',4,'Duration', RightValveTime,'OnsetDelay',0,...
  530. 'Channel', 'Valve3', 'OnMessage', 1, 'OffMessage', 0, 'Loop',...
  531. RightRewardDrops, 'SendEvents', 1, 'LoopInterval', RewardPauseTime,'OnsetTrigger', '10');
  532. sma = SetGlobalCounter(sma, 4, 'GlobalTimer4_End', RightRewardDrops);
  533. elseif RightRewardDrops == 1
  534. sma = SetGlobalTimer(sma,'TimerID',4,'Duration',RightValveTime,'OnsetDelay',0,...
  535. 'Channel', 'Valve3', 'OnMessage', 1, 'OffMessage', 0, 'Loop', 0, 'SendEvents', 1,'LoopInterval',0,'OnsetTrigger', '10');
  536. sma = SetGlobalCounter(sma, 4, 'GlobalTimer4_End', 1);
  537. else
  538. sma = SetGlobalTimer(sma,'TimerID',4,'Duration',0,'OnsetDelay',0,...
  539. 'Channel', 'Valve3', 'OnMessage', 0, 'OffMessage', 0, 'Loop', 0, 'SendEvents', 1,'LoopInterval',0,'OnsetTrigger', '10');
  540. sma = SetGlobalCounter(sma, 4, 'GlobalTimer4_End', 1);
  541. end
  543. sma = SetGlobalTimer(sma, 'TimerID', 7,...
  544. 'Duration',0.01, 'OnsetDelay', 0,...
  545. 'Channel', 'BNC1', 'OnMessage', 1,...
  546. 'OffMessage', 0, 'Loop', 1,...
  547. 'SendEvents', 1, 'LoopInterval', 0.1);
  549. % sma = SetGlobalTimer(sma, 'TimerID', 8,...
  550. % 'Duration',0.1, 'OnsetDelay', 0,...
  551. % 'Channel', 'BNC2', 'OnMessage', 1,...
  552. % 'OffMessage', 0, 'Loop', 0,...
  553. % 'SendEvents', 1);
  555. sma = SetGlobalTimer(sma, 'TimerID', 8, 'Duration', 0.01, 'OnsetDelay', 0,...
  556. 'Channel', 'BNC2', 'OnLevel', 1, 'OffLevel', 0,...
  557. 'Loop', 1, 'SendGlobalTimerEvents', 1, 'LoopInterval', 0.04);
  559. % STATES
  560. sma = AddState(sma, 'Name', 'TimerStart', ...
  561. 'Timer', 0,...
  562. 'StateChangeConditions', {'Tup', 'InterTrialInterval'},...
  563. 'OutputActions', {'GlobalTimerTrig',7,'HiFi1','*'});
  564. sma = AddState(sma, 'Name', 'InterTrialInterval', ...
  565. 'Timer', S.GUI.Interval,...
  566. 'StateChangeConditions', {'Tup', 'StartTrial'},...
  567. 'OutputActions', {'GlobalTimerTrig',8});
  568. sma = AddState(sma, 'Name', 'StartTrial', ...
  569. 'Timer', 0,...
  570. 'StateChangeConditions', {'Tup', 'WaitForCenter'},...
  571. 'OutputActions', {});
  572. sma = AddState(sma, 'Name', 'WaitForCenter', ...
  573. 'Timer', 0,...
  574. 'StateChangeConditions', {'Port2In', 'CenterDelay','Condition2','CenterDelay'},... % test how these are different!
  575. 'OutputActions', {'PWM2',50}); % port light on
  576. sma = AddState(sma, 'Name', 'CenterDelay', ...
  577. 'Timer', S.GUI.CenterDelay,...
  578. 'StateChangeConditions', {'Tup', 'CenterOdor','Port2Out','WaitForCenter'},...
  579. 'OutputActions', {'PWM2',50});
  580. sma = AddState(sma, 'Name', 'CenterOdor', ...
  581. 'Timer', S.GUI.CenterOdorTime,...
  582. 'StateChangeConditions', {'Port2Out', 'CenterOdorOff', 'Tup', 'CenterPostOdorDelay'},...
  583. 'OutputActions',[{DIOmodule,3,'PWM2',50},RunOdor(ThisCenterOdor,0)]);
  584. sma = AddState(sma, 'Name', 'CenterOdorOff',...
  585. 'Timer', 0,...
  586. 'StateChangeConditions', {'Tup','WaitForCenter'},...
  587. 'OutputActions', [{DIOmodule,4,'PWM2',50},RunOdor(ThisCenterOdor,0)]);
  588. sma = AddState(sma, 'Name', 'CenterPostOdorDelay', ...
  589. 'Timer', S.GUI.StartDelay,...
  590. 'StateChangeConditions', {'Port2Out','WaitForCenter','Tup','GoCue'},... % is that right?
  591. 'OutputActions', [{DIOmodule,4,'PWM2',50},RunOdor(ThisCenterOdor,0)]);
  592. sma = AddState(sma, 'Name', 'GoCue', ...
  593. 'Timer', 0.05,...
  594. 'StateChangeConditions', {'Tup','Response'},...
  595. 'OutputActions', {'GlobalTimerTrig',1,'HiFi1', ['P' 2]});
  597. % RESPONSE (CHOICE) --> MAKE SURE STAY IN SIDE FOR AT LEAST A SMALL TIME TO INDICATE CHOICE?
  598. sma = AddState(sma, 'Name', 'Response', ...
  599. 'Timer', S.GUI.OdorDelay,...
  600. 'StateChangeConditions', {'Tup','GracePeriod','Port1In',ChooseLeft,'Port3In',ChooseRight},...
  601. 'OutputActions', {});
  603. sma = AddState(sma, 'Name', 'GracePeriod',...
  604. 'Timer', S.GUI.GracePeriod,...
  605. 'StateChangeConditions', {'Tup','NoChoice','Port1In',ChooseLeft,'Port3In',ChooseRight},...
  606. 'OutputActions', {});
  608. % AFTER CHOICE
  610. % LEFT
  611. sma = AddState(sma, 'Name', 'WaitForOdorLeft', ...
  612. 'Timer', 0,...
  613. 'StateChangeConditions', {'GlobalTimer1_End',SideOdorStateLeft,'Condition7',SideOdorStateLeft},...
  614. 'OutputActions', {});
  615. sma = AddState(sma, 'Name', 'OdorALeft', ...
  616. 'Timer', S.GUI.OdorTime,...
  617. 'StateChangeConditions', {'Tup','RewardDelayLeft'},...
  618. 'OutputActions', [{DIOmodule,5}, RunOdor(LeftSideOdor,1)]);
  619. sma = AddState(sma, 'Name', 'OdorBLeft', ...
  620. 'Timer', S.GUI.OdorTime,...
  621. 'StateChangeConditions', {'Tup','RewardDelayLeft'},...
  622. 'OutputActions', [{DIOmodule,5}, RunOdor(LeftSideOdor,1)]);
  623. sma = AddState(sma, 'Name', 'OdorCLeft', ...
  624. 'Timer', S.GUI.OdorTime,...
  625. 'StateChangeConditions', {'Tup','RewardDelayLeft'},...
  626. 'OutputActions', [{DIOmodule,5}, RunOdor(LeftSideOdor,1)]);
  627. sma = AddState(sma, 'Name', 'OdorDLeft', ...
  628. 'Timer', S.GUI.OdorTime,...
  629. 'StateChangeConditions', {'Tup','RewardDelayLeft'},...
  630. 'OutputActions', [{DIOmodule,5}, RunOdor(LeftSideOdor,1)]);
  631. sma = AddState(sma, 'Name', 'OdorWaterLeft', ...
  632. 'Timer', S.GUI.OdorTime,...
  633. 'StateChangeConditions', {'Tup','RewardDelayWaterLeft'},...
  634. 'OutputActions', {DIOmodule,5});
  635. sma = AddState(sma, 'Name', 'RewardDelayWaterLeft', ...
  636. 'Timer', DelayTime,...
  637. 'StateChangeConditions', {'Tup','LeftWarning'},...
  638. 'OutputActions', {DIOmodule,6});
  639. sma = AddState(sma, 'Name', 'RewardDelayLeft', ...
  640. 'Timer', DelayTime,...
  641. 'StateChangeConditions', {'Tup','LeftWarning'},...
  642. 'OutputActions', [{DIOmodule,6}, RunOdor(LeftSideOdor,1)]);
  644. % LEFT REWARD
  645. sma = AddState(sma, 'Name', 'LeftWarning', ...
  646. 'Timer', WarningTime,...
  647. 'StateChangeConditions', {'Tup','LeftPortCheck'},...
  648. 'OutputActions', [{'PWM1',50},ToneCmd]);
  649. sma = AddState(sma, 'Name', 'LeftPortCheck',...
  650. 'Timer',0,...
  651. 'StateChangeConditions',{'Condition4','LeftNotPresent','Condition1',OutcomeStateLeft},...
  652. 'OutputActions',{});
  653. sma = AddState(sma, 'Name', 'LeftBigReward', ...
  654. 'Timer', 0,...
  655. 'StateChangeConditions', {'Tup','OutcomeDelivery','Condition4','LeftNotPresent'},...
  656. 'OutputActions', {'GlobalTimerTrig', 3}); %, 'GlobalTimerTrig', 3
  657. sma = AddState(sma, 'Name', 'LeftSmallReward', ...
  658. 'Timer', 0,...
  659. 'StateChangeConditions', {'Tup','OutcomeDelivery','Condition4','LeftNotPresent'},...
  660. 'OutputActions', {'GlobalTimerTrig', 3}); %, 'GlobalTimerTrig', 3
  661. sma = AddState(sma, 'Name', 'LeftNotPresent', ...
  662. 'Timer', 0,...
  663. 'StateChangeConditions', {'Tup','OutcomeDelivery'},...
  664. 'OutputActions', {'GlobalTimerTrig', 2});
  667. % CHOOSE RIGHT
  668. sma = AddState(sma, 'Name', 'WaitForOdorRight', ...
  669. 'Timer', 0,...
  670. 'StateChangeConditions', {'GlobalTimer1_End',SideOdorStateRight,'Condition7',SideOdorStateRight},...
  671. 'OutputActions', {});
  672. sma = AddState(sma, 'Name', 'OdorARight', ...
  673. 'Timer', S.GUI.OdorTime,...
  674. 'StateChangeConditions', {'Tup','RewardDelayRight'},...
  675. 'OutputActions', [{DIOmodule,5}, RunOdor(RightSideOdor,2)]);
  676. sma = AddState(sma, 'Name', 'OdorBRight', ...
  677. 'Timer', S.GUI.OdorTime,...
  678. 'StateChangeConditions', {'Tup','RewardDelayRight'},...
  679. 'OutputActions', [{DIOmodule,5}, RunOdor(RightSideOdor,2)]);
  680. sma = AddState(sma, 'Name', 'OdorCRight', ...
  681. 'Timer', S.GUI.OdorTime,...
  682. 'StateChangeConditions', {'Tup','RewardDelayRight'},...
  683. 'OutputActions', [{DIOmodule,5}, RunOdor(RightSideOdor,2)]);
  684. sma = AddState(sma, 'Name', 'OdorDRight', ...
  685. 'Timer', S.GUI.OdorTime,...
  686. 'StateChangeConditions', {'Tup','RewardDelayRight'},...
  687. 'OutputActions', [{DIOmodule,5}, RunOdor(RightSideOdor,2)]);
  688. sma = AddState(sma, 'Name', 'OdorWaterRight', ...
  689. 'Timer', S.GUI.OdorTime,...
  690. 'StateChangeConditions', {'Tup','RewardDelayWaterRight'},...
  691. 'OutputActions', {DIOmodule,5});
  692. sma = AddState(sma, 'Name', 'RewardDelayWaterRight', ...
  693. 'Timer', DelayTime,...
  694. 'StateChangeConditions', {'Tup','RightWarning'},...
  695. 'OutputActions', {DIOmodule,6});
  696. sma = AddState(sma, 'Name', 'RewardDelayRight', ...
  697. 'Timer', DelayTime,...
  698. 'StateChangeConditions', {'Tup','RightWarning'},...
  699. 'OutputActions', [{DIOmodule,6}, RunOdor(RightSideOdor,2)]);
  701. % RIGHT REWARD
  702. sma = AddState(sma, 'Name', 'RightWarning', ...
  703. 'Timer', WarningTime,...
  704. 'StateChangeConditions', {'Tup','RightPortCheck'},...
  705. 'OutputActions', [{'PWM3',50},ToneCmd]);
  706. sma = AddState(sma, 'Name', 'RightPortCheck',...
  707. 'Timer',0,...
  708. 'StateChangeConditions',{'Condition6','RightNotPresent','Condition3',OutcomeStateRight},...
  709. 'OutputActions',{});
  710. sma = AddState(sma, 'Name', 'RightBigReward', ...
  711. 'Timer', 0,...
  712. 'StateChangeConditions', {'Tup','OutcomeDelivery','Condition6','RightNotPresent'},...
  713. 'OutputActions', {'GlobalTimerTrig', 4}); %, 'GlobalTimerTrig', 4
  714. sma = AddState(sma, 'Name', 'RightSmallReward', ...
  715. 'Timer', 0,...
  716. 'StateChangeConditions', {'Tup','OutcomeDelivery','Condition6','RightNotPresent'},...
  717. 'OutputActions', {'GlobalTimerTrig', 4}); %, 'GlobalTimerTrig', 4
  718. sma = AddState(sma, 'Name', 'RightNotPresent', ...
  719. 'Timer', 0,...
  720. 'StateChangeConditions', {'Tup','OutcomeDelivery'},...
  721. 'OutputActions', {'GlobalTimerTrig', 2});
  723. % Waits for max drops time
  724. sma = AddState(sma, 'Name','OutcomeDelivery','Timer',0,...
  725. 'StateChangeConditions',{'GlobalCounter2_End','EndTrial'},...
  726. 'OutputActions',{});
  728. % if no choice during response
  729. sma = AddState(sma, 'Name', 'NoChoice', ...
  730. 'Timer', 0,...
  731. 'StateChangeConditions', {'GlobalTimer1_End', 'TimeoutOdor', 'Condition7', 'TimeoutOdor'},...
  732. 'OutputActions', {});
  734. % For incorrect choices (left/right on forced trials)
  735. sma = AddState(sma, 'Name', 'Incorrect', ...
  736. 'Timer', 0,...
  737. 'StateChangeConditions', {'GlobalTimer1_End','TimeoutOdor','Condition7', 'TimeoutOdor'},...
  738. 'OutputActions', {});
  740. sma = AddState(sma, 'Name', 'TimeoutOdor', ...
  741. 'Timer', S.GUI.OdorTime,...
  742. 'StateChangeConditions', {'Tup','TimeoutRewardDelay'},...
  743. 'OutputActions', {});
  744. sma = AddState(sma, 'Name', 'TimeoutRewardDelay', ...
  745. 'Timer', S.GUI.RewardDelay,...
  746. 'StateChangeConditions', {'Tup','TimeoutPortCheck'},...
  747. 'OutputActions', {});
  748. sma = AddState(sma, 'Name', 'TimeoutPortCheck', ...
  749. 'Timer', 0,...
  750. 'StateChangeConditions', {'Tup','TimeoutOutcome'},...
  751. 'OutputActions', {});
  752. sma = AddState(sma, 'Name', 'TimeoutOutcome', ...
  753. 'Timer', 0,...
  754. 'StateChangeConditions', {'GlobalCounter2_End','EndTrial'},...
  755. 'OutputActions', {'GlobalTimerTrig', 2});
  757. sma = AddState(sma, 'Name', 'EndTrial', ...
  758. 'Timer', 1,...
  759. 'StateChangeConditions', {'Tup', '>exit'},...
  760. 'OutputActions', {'GlobalTimerCancel',2});
  761. end
  763. %% TRIAL TYPES
  765. function S = UpdateTrialTypes(i,S)
  766. % Insert a repeat of trial i-1 at position i, shifting everything else forward.
  767. % Called when a mouse enters a side port before odor delivery, to re-present
  768. % the current trial type before advancing.
  769. TrialTypes = S.TrialTypes;
  770. S.TrialTypes = [TrialTypes(1:i-1); TrialTypes(i-1); TrialTypes(i:end-1)];
  771. S.RewardTypes = [S.RewardTypes(1:i-1,:); S.RewardTypes(i-1,:); S.RewardTypes(i:end-1,:)];
  772. S.RandOdorTypes = [S.RandOdorTypes(1:i-1); S.RandOdorTypes(i-1); S.RandOdorTypes(i:end-1)];
  773. end
  775. function S = SetTrialTypes(S,currentTrial)
  776. % Build S.TrialTypes array from currentTrial to SessionTrials.
  777. % Trial types (1=Small, 2=Info, 3=Rand, 4=Big) are shuffled in blocks of blockSize
  778. % according to the percentages set by S.GUI.TrialTypes.
  780. global BpodSystem;
  782. %% Define trial choice types
  784. maxTrials = S.GUI.SessionTrials;
  786. typesAvailable = S.GUI.TrialTypes;
  788. blockSize = 12;
  789. blockToShuffle = zeros(blockSize,1);
  790. typeBlockSize = 8;
  791. bigPercent = 0; smallPercent = 0; infoPercent = 0; randPercent = 0;
  793. switch typesAvailable
  794. case 1
  795. smallPercent = 1; bigPercent = 0; infoPercent = 0; randPercent = 0;
  796. blockToShuffle = [1 1 1 1 1 1 1 1 1 1 1 1];
  797. case 2
  798. smallPercent = 0; bigPercent = 0; infoPercent = 1; randPercent = 0;
  799. blockToShuffle = [2 2 2 2 2 2 2 2 2 2 2 2];
  800. case 3
  801. smallPercent = 0; bigPercent = 0; infoPercent = 0; randPercent = 1;
  802. blockToShuffle = [3 3 3 3 3 3 3 3 3 3 3 3];
  803. case 4
  804. smallPercent = 0; bigPercent = 1; infoPercent = 0; randPercent = 0;
  805. blockToShuffle = [4 4 4 4 4 4 4 4 4 4 4 4];
  806. case 5
  807. smallPercent = 0.25; bigPercent = 0.25; infoPercent = 0.25; randPercent = 0.25;
  808. blockToShuffle = [1 1 1 2 2 2 3 3 3 4 4 4];
  809. case 6
  810. smallPercent = 0.5; bigPercent = 0.5; infoPercent = 0; randPercent = 0;
  811. blockToShuffle = [1 1 1 1 1 1 4 4 4 4 4 4];
  812. case 7
  813. smallPercent = 0.5; bigPercent = 0; infoPercent = 0.5; randPercent = 0;
  814. blockToShuffle = [1 1 1 1 1 1 2 2 2 2 2 2];
  815. case 8
  816. smallPercent = 0; bigPercent = 0.5; infoPercent = 0; randPercent = 0.5;
  817. blockToShuffle = [4 4 4 4 4 4 3 3 3 3 3 3];
  818. end
  820. blocks = ceil(maxTrials/blockSize);
  821. TrialTypes = zeros(blocks*blockSize,1);
  823. block=blockToShuffle;
  825. for n = 1:blocks
  826. for m = 1:blockSize
  827. i = randi(blockSize);
  828. temp = block(m);
  829. block(m) = block(i);
  830. block(i) = temp;
  831. end
  832. if n == 1
  833. TrialTypes(1:blockSize) = block;
  834. else
  835. TrialTypes((n-1)*blockSize+1:n*blockSize) = block;
  836. end
  837. end
  839. % TrialTypes = [2; 2; 3; 3; 2; 2; 3; 3; TrialTypes];
  840. TrialTypes=TrialTypes(1:maxTrials);
  841. if currentTrial==1
  842. S.TrialTypes = TrialTypes;
  843. else
  844. S.TrialTypes = [S.TrialTypes(1:currentTrial-1); TrialTypes(1:end-currentTrial+1)];
  845. TrialTypePlotInfoWater(BpodSystem.GUIHandles.TrialTypePlot,'update',currentTrial,S.TrialTypes);
  846. end
  849. end
  851. function S = SetRewardTypes(S,currentTrial)
  852. % Build S.RewardTypes (Nx2 matrix) and S.RandOdorTypes (Nx1) from currentTrial to SessionTrials.
  853. % Columns of RewardTypes: [InfoForced, RandForced] — each column holds a shuffled
  854. % list of 1s (big) and 0s (small) per block, giving the reward size for each
  855. % successive Info or Rand forced trial.
  857. maxTrials = S.GUI.SessionTrials;
  858. typeBlockSize = 8;
  860. %% SET REWARD BLOCKS
  862. infoBigCount = round(S.GUI.InfoRewardProb*typeBlockSize);
  863. randBigCount = round(S.GUI.RandRewardProb*typeBlockSize);
  865. infoBlockShuffle = zeros(typeBlockSize,1);
  866. randBlockShuffle = zeros(typeBlockSize,1);
  867. randOdorBlockShuffle = zeros(typeBlockSize,1);
  869. infoBlockShuffle(1:infoBigCount) = 1;
  870. randBlockShuffle(1:randBigCount) = 1;
  872. if S.GUI.RandRewardProb == 0 | S.GUI.RandRewardProb == 1
  873. randOdorBigCount = ceil(typeBlockSize/2);
  874. else
  875. randOdorBigCount = randBigCount;
  876. end
  877. randOdorBlockShuffle(1:randOdorBigCount) = 1;
  879. typeBlockCount = ceil(maxTrials/typeBlockSize);
  880. RewardTypes = zeros(typeBlockCount*typeBlockSize,2);
  881. RandOdorTypes = zeros(typeBlockCount*typeBlockSize,1);
  883. infoBlock = infoBlockShuffle;
  884. randBlock = randBlockShuffle;
  885. randOdorBlock = randOdorBlockShuffle;
  887. % info forced
  888. for n = 1:typeBlockCount
  889. for m = 1:typeBlockSize
  890. i = randi(typeBlockSize);
  891. temp = infoBlock(m);
  892. infoBlock(m) = infoBlock(i);
  893. infoBlock(i) = temp;
  894. end
  895. if n == 1
  896. RewardTypes(1:typeBlockSize,1) = infoBlock';
  897. else
  898. RewardTypes((n-1)*typeBlockSize+1:n*typeBlockSize,1) = infoBlock';
  899. end
  900. end
  902. % rand forced
  903. for n = 1:typeBlockCount
  904. for m = 1:typeBlockSize
  905. i = randi(typeBlockSize);
  906. temp = randBlock(m);
  907. randBlock(m) = randBlock(i);
  908. randBlock(i) = temp;
  909. end
  910. if n == 1
  911. RewardTypes(1:typeBlockSize,2) = randBlock';
  912. else
  913. RewardTypes((n-1)*typeBlockSize+1:n*typeBlockSize,2) = randBlock';
  914. end
  915. end
  917. % rand odors
  918. for n = 1:typeBlockCount
  919. for m = 1:typeBlockSize
  920. i = randi(typeBlockSize);
  921. temp = randOdorBlock(m);
  922. randOdorBlock(m) = randOdorBlock(i);
  923. randOdorBlock(i) = temp;
  924. end
  925. if n == 1
  926. RandOdorTypes(1:typeBlockSize) = randOdorBlock';
  927. else
  928. RandOdorTypes((n-1)*typeBlockSize+1:n*typeBlockSize) = randOdorBlock';
  929. end
  930. end
  932. % Trial types (rewards) to pull from
  933. RewardTypes = RewardTypes(1:maxTrials,:);
  935. % Rand Odors to pull from
  936. % RandOdorTypes = repmat(RandOdorTypes,1,4);
  937. RandOdorTypes = RandOdorTypes(1:maxTrials);
  939. if currentTrial == 1
  940. S.RandOdorTypes = RandOdorTypes;
  941. S.RewardTypes = RewardTypes;
  942. else
  943. S.RandOdorTypes = [S.RandOdorTypes(1:currentTrial); RandOdorTypes(1:end-currentTrial)];
  944. S.RewardTypes = [S.RewardTypes(1:currentTrial,:); RewardTypes(1:end-currentTrial,:)];
  945. end
  946. end
  948. %% ODOR CONTROL
  950. function OdorOutputActions = RunOdor(odorID,port)
  951. % Return the {module, valve} output action pairs needed to route odorID through port.
  952. % port: 0=center, 1=left, 2=right
  953. % odorID: 0-3 maps to physical valve positions on ValveModule2/3
  954. switch port
  955. case 0
  956. cmd1 = {'ValveModule1',1}; % center control
  957. switch odorID
  958. case 0
  959. cmd2 = {'ValveModule2',1};
  960. cmd3 = {'ValveModule3',1};
  961. case 1
  962. cmd2 = {'ValveModule2',2};
  963. cmd3 = {'ValveModule3',2};
  964. case 2
  965. cmd2 = {'ValveModule2',3};
  966. cmd3 = {'ValveModule3',3};
  967. case 3
  968. cmd2 = {'ValveModule2',4};
  969. cmd3 = {'ValveModule3',4};
  970. end
  971. case 1 % LEFT
  972. cmd1 = {'ValveModule1',2}; % left control
  973. switch odorID
  974. case 0
  975. cmd2 = {'ValveModule2',5};
  976. cmd3 = {'ValveModule3',5};
  977. case 1
  978. cmd2 = {'ValveModule2',6};
  979. cmd3 = {'ValveModule3',6};
  980. case 2
  981. cmd2 = {'ValveModule2',7};
  982. cmd3 = {'ValveModule3',7};
  983. case 3
  984. cmd2 = {'ValveModule2',8};
  985. cmd3 = {'ValveModule3',8};
  986. end
  987. case 2 % RIGHT
  988. cmd1 = {'ValveModule1',3}; % right control
  989. switch odorID
  990. case 0
  991. cmd2 = {'ValveModule2',5};
  992. cmd3 = {'ValveModule3',5};
  993. case 1
  994. cmd2 = {'ValveModule2',6};
  995. cmd3 = {'ValveModule3',6};
  996. case 2
  997. cmd2 = {'ValveModule2',7};
  998. cmd3 = {'ValveModule3',7};
  999. case 3
  1000. cmd2 = {'ValveModule2',8};
  1001. cmd3 = {'ValveModule3',8};
  1002. end
  1003. end
  1004. OdorOutputActions = [cmd1,cmd2,cmd3];
  1005. end
  1007. function TurnOffAllOdors()
  1008. % Close all 8 positions on all three valve modules. Called on session end or abort.
  1009. for v = 1:8
  1010. ModuleWrite('ValveModule1',['C' v]);
  1011. ModuleWrite('ValveModule2',['C' v]);
  1012. ModuleWrite('ValveModule3',['C' v]);
  1013. end
  1014. end
  1016. %% SET ODOR SIDES (LATCH VALVES)
  1017. function SetLatchValves(S)
  1018. % Configure DIOmodule connections to H-bridge powering of Lee Company latch valves to route odors to the correct ports
  1019. % based on S.GUI.InfoSide (0=info→left, 1=info→right).
  1020. global BpodSystem
  1022. infoSide = S.GUI.InfoSide;
  1023. modules = BpodSystem.Modules.Name;
  1024. % latchValves = [16 15 14 11 10 9 8 7]; % evens to left!
  1025. latchModule = [modules(strncmp('DIO',modules,3))];
  1026. latchModule = latchModule{1};
  1028. % now, latch odds to the left. for 0, 1, 2, 3
  1029. latchValves = [7 8 9 10 11 14 15 16]; % evens to left! odor 0 left, odor 0 right, odor 1 left,
  1031. if infoSide == 0 % SEND INFO ODORS TO LEFT (A,B)
  1032. odorApin = latchValves((S.GUI.OdorA+1)*2-1);
  1033. odorBpin = latchValves((S.GUI.OdorB+1)*2-1);
  1034. odorCpin = latchValves((S.GUI.OdorC+1)*2);
  1035. odorDpin = latchValves((S.GUI.OdorD+1)*2);
  1036. else
  1037. odorApin = latchValves((S.GUI.OdorA+1)*2);
  1038. odorBpin = latchValves((S.GUI.OdorB+1)*2);
  1039. odorCpin = latchValves((S.GUI.OdorC+1)*2-1);
  1040. odorDpin = latchValves((S.GUI.OdorD+1)*2-1);
  1041. end
  1043. pins = [odorApin odorBpin odorCpin odorDpin];
  1045. for i = 1:4
  1046. ModuleWrite(latchModule,[pins(i) 1]);
  1047. pause(100/1000);
  1048. ModuleWrite(latchModule,[pins(i) 0]);
  1049. pause(100/1000);
  1050. end
  1052. % BpodSystem.GUIHandles.EventsPlot.StateColors = getStateColors(infoSide);
  1053. % EventsPlot('init', getStateColors(infoSide));
  1054. end
  1056. %% OUTCOME
  1058. function [rewardAmount, Outcome] = UpdateOutcome(currentTrial,S,RewardLeft,RewardRight)
  1059. % Determine outcome code and reward amount from the completed trial's raw events.
  1060. % RewardLeft/RewardRight: reward size (big=1, small=0) pre-computed for this trial
  1061. % (only meaningful for Info/Rand forced trials; Small/Big trials have a fixed size).
  1062. % Outcome codes are defined in the file header.
  1063. % Updates BpodSystem.Data.TrialCounts and .PlotOutcomes in place.
  1065. global BpodSystem
  1066. % BpodSystem.Data.RawEvents(currentTrial)
  1067. TrialData = BpodSystem.Data.RawEvents.Trial{currentTrial};
  1068. TrialCounts = BpodSystem.Data.TrialCounts;
  1069. PlotOutcomes = BpodSystem.Data.PlotOutcomes;
  1071. trialType = S.TrialTypes(currentTrial);
  1072. infoSide = S.GUI.InfoSide;
  1073. bigSide = S.GUI.BigSide;
  1074. infoBigReward = S.GUI.InfoBigDrops*4;
  1075. infoSmallReward = S.GUI.InfoSmallDrops*4;
  1076. randBigReward = S.GUI.RandBigDrops*4;
  1077. randSmallReward = S.GUI.RandSmallDrops*4;
  1078. bigReward = S.GUI.BigDrops*4;
  1079. smallReward = S.GUI.SmallDrops*4;
  1080. rewardAmount = 0;
  1081. x = currentTrial;
  1082. newTrialCounts = TrialCounts;
  1083. newPlotOutcomes = PlotOutcomes;
  1085. % Plot outcomes: 2 = no choice, incorrect, info correct, rand correct,
  1086. % not present
  1088. % change to no choice, incorrect, info correct big info correct small
  1089. % rand correct big/ not present info big not present info small
  1091. switch trialType
  1092. case 1
  1093. if bigSide == 0
  1094. if ~isnan(TrialData.States.NoChoice(1))
  1095. newPlotOutcomes(x) = 14;
  1096. Outcome = 1; % small no choice
  1097. elseif ~isnan(TrialData.States.WaitForOdorRight(1))
  1098. newTrialCounts(1) = TrialCounts(1) + 1; % small
  1099. if ~isnan(TrialData.States.RightSmallReward(1))
  1100. Outcome = 2; % small correct
  1101. rewardAmount = smallReward;
  1102. newPlotOutcomes(x) = 10;
  1103. else
  1104. newPlotOutcomes(x) = 12;
  1105. Outcome = 3; % small NP
  1106. end
  1107. else
  1108. Outcome = 4; % small incorrect
  1109. newPlotOutcomes(x) = 13;
  1110. end
  1111. else
  1112. if ~isnan(TrialData.States.NoChoice(1))
  1113. newPlotOutcomes(x) = 14;
  1114. Outcome = 1; % small no choice
  1115. elseif ~isnan(TrialData.States.WaitForOdorLeft(1))
  1116. newTrialCounts(1) = TrialCounts(1) + 1; % small
  1117. if ~isnan(TrialData.States.LeftSmallReward(1))
  1118. Outcome = 2; % small correct
  1119. rewardAmount = smallReward;
  1120. newPlotOutcomes(x) = 10;
  1121. else
  1122. newPlotOutcomes(x) = 12;
  1123. Outcome = 3; % small NP
  1124. end
  1125. else
  1126. Outcome = 4; % small incorrect
  1127. newPlotOutcomes(x) = 13;
  1128. end
  1129. end
  1131. case 2 % INFO
  1132. if ~isnan(TrialData.States.NoChoice(1))
  1133. newPlotOutcomes(x) = 14;
  1134. Outcome = 5; % info no choice
  1135. elseif infoSide==0 & ~isnan(TrialData.States.WaitForOdorLeft(1))
  1136. newTrialCounts(2) = TrialCounts(2) + 1; % infoforced
  1137. if RewardLeft == 1
  1138. if ~isnan(TrialData.States.LeftBigReward(1))
  1139. Outcome = 6; % info big
  1140. rewardAmount = infoBigReward;
  1141. newPlotOutcomes(x) = 1;
  1142. else
  1143. newPlotOutcomes(x) = 5;
  1144. Outcome = 7; % info big NP
  1145. end
  1146. else
  1147. if ~isnan(TrialData.States.LeftSmallReward(1))
  1148. Outcome = 8; % info small
  1149. rewardAmount = infoSmallReward;
  1150. newPlotOutcomes(x) = 2;
  1151. else
  1152. newPlotOutcomes(x) = 6;
  1153. Outcome = 9; % info small NP
  1154. end
  1155. end
  1156. elseif infoSide==1 & ~isnan(TrialData.States.WaitForOdorRight(1))
  1157. newTrialCounts(2) = TrialCounts(2) + 1; % infoforced
  1158. if RewardRight == 1
  1159. if ~isnan(TrialData.States.RightBigReward(1))
  1160. Outcome = 6; % info big
  1161. rewardAmount = infoBigReward;
  1162. newPlotOutcomes(x) = 1;
  1163. else
  1164. newPlotOutcomes(x) = 5;
  1165. Outcome = 7; % info big NP
  1166. end
  1167. else
  1168. if ~isnan(TrialData.States.RightSmallReward(1))
  1169. Outcome = 8; % info small
  1170. rewardAmount = infoSmallReward;
  1171. newPlotOutcomes(x) = 2;
  1172. else
  1173. newPlotOutcomes(x) = 6;
  1174. Outcome = 9; % info small NP
  1175. end
  1176. end
  1177. else
  1178. newTrialCounts(2) = TrialCounts(2) + 1; % infoforced
  1179. newPlotOutcomes(x) = 13;
  1180. Outcome = 10; % info incorrect
  1181. end
  1183. case 3 %NO INFO
  1184. if ~isnan(TrialData.States.NoChoice(1))
  1185. newPlotOutcomes(x) = 14;
  1186. Outcome = 11; % rand no choice
  1187. elseif infoSide==0 & ~isnan(TrialData.States.WaitForOdorRight(1))
  1188. newTrialCounts(3) = TrialCounts(3) + 1; % randforced
  1189. if RewardRight == 1
  1190. if ~isnan(TrialData.States.RightBigReward(1))
  1191. Outcome = 12; % rand big
  1192. rewardAmount = randBigReward;
  1193. newPlotOutcomes(x) = 3;
  1194. else
  1195. newPlotOutcomes(x) = 7;
  1196. Outcome = 13; % rand big NP
  1197. end
  1198. else
  1199. if ~isnan(TrialData.States.RightSmallReward(1))
  1200. Outcome = 14; % rand small
  1201. rewardAmount = randSmallReward;
  1202. newPlotOutcomes(x) = 4;
  1203. else
  1204. newPlotOutcomes(x) = 8;
  1205. Outcome = 15; % rand small NP
  1206. end
  1207. end
  1208. elseif infoSide==1 & ~isnan(TrialData.States.WaitForOdorLeft(1))
  1209. newTrialCounts(3) = TrialCounts(3) + 1; % randforced
  1210. if RewardLeft == 1
  1211. if ~isnan(TrialData.States.LeftBigReward(1))
  1212. Outcome = 12; % rand big
  1213. rewardAmount = randBigReward;
  1214. newPlotOutcomes(x) = 3;
  1215. else
  1216. newPlotOutcomes(x) = 7;
  1217. Outcome = 13; % rand big NP
  1218. end
  1219. else
  1220. if ~isnan(TrialData.States.LeftSmallReward(1))
  1221. Outcome = 14; % rand small
  1222. rewardAmount = randSmallReward;
  1223. newPlotOutcomes(x) = 4;
  1224. else
  1225. newPlotOutcomes(x) = 8;
  1226. Outcome = 15; % rand small NP
  1227. end
  1228. end
  1229. else
  1230. newTrialCounts(3) = TrialCounts(3) + 1; % rand forced
  1231. newPlotOutcomes(x) = 13;
  1232. Outcome = 16; % rand incorrect
  1233. end
  1235. case 4 % BIG WATER
  1236. if bigSide == 0
  1237. if ~isnan(TrialData.States.NoChoice(1))
  1238. newPlotOutcomes(x) = 14;
  1239. Outcome = 17; % big no choice
  1240. elseif ~isnan(TrialData.States.WaitForOdorLeft(1))
  1241. newTrialCounts(4) = TrialCounts(4) + 1; % big
  1242. if ~isnan(TrialData.States.LeftBigReward(1))
  1243. Outcome = 18; % big correct
  1244. rewardAmount = bigReward;
  1245. newPlotOutcomes(x) = 9;
  1246. else
  1247. newPlotOutcomes(x) = 11;
  1248. Outcome = 19; % big NP
  1249. end
  1250. else
  1251. Outcome = 20; % big incorrect
  1252. newPlotOutcomes(x) = 13;
  1253. end
  1254. else
  1255. if ~isnan(TrialData.States.NoChoice(1))
  1256. newPlotOutcomes(x) = 14;
  1257. Outcome = 17; % big no choice
  1258. elseif ~isnan(TrialData.States.WaitForOdorRight(1))
  1259. newTrialCounts(4) = TrialCounts(4) + 1; % big
  1260. if ~isnan(TrialData.States.RightBigReward(1))
  1261. Outcome = 18; % big correct
  1262. rewardAmount = bigReward;
  1263. newPlotOutcomes(x) = 9;
  1264. else
  1265. newPlotOutcomes(x) = 11;
  1266. Outcome = 19; % big NP
  1267. end
  1268. else
  1269. Outcome = 20; % big incorrect
  1270. newPlotOutcomes(x) = 13;
  1271. end
  1272. end
  1273. end
  1274. BpodSystem.Data.TrialCounts = newTrialCounts;
  1275. BpodSystem.Data.PlotOutcomes = newPlotOutcomes;
  1276. end

InfoseekWaterVal.m at commit 1f3cffd, no license · at the source

Overview

Authors: Jennifer J Bussell1,2, Ryan P Badman3,4, David Márton3, Ethan S Bromberg-Martin5, L F Abbott1,2,6, Kanaka Rajan3,4, Richard Axel1,2,6
ORCID iDs: Jennifer J Bussell, Ryan P Badman, David Márton, Ethan S Bromberg-Martin, L F Abbott, Kanaka Rajan, Richard Axel
  1. Department of Neuroscience, Columbia University, New York, NY USA
  2. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY USA
  3. Department of Neurobiology, Harvard Medical School, Boston, MA USA
  4. Kempner Institute, Harvard University, Cambridge, MA USA
  5. Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD USA
  6. Kavli Institute for Brain Science, Columbia University, New York, NY USA
Institutions: Mortimer B. Zuckerman Mind Brain Behavior Institute (United States); Columbia University (United States); Harvard University (United States); Johns Hopkins University (United States)
Journal: Nature neuroscience, volume 29, issue 9, pages 2261-2272
Dates: received 4 November 2024; accepted 12 June 2026; published online 30 July 2026; in print 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s41593-026-02377-y · PMID 42533133 · PMCID PMC13533842 · OpenAlex W7171881172
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: mouse (organism), systems (subfield)
Methods: Connectivity, Statistics, Smoothing, state filtering, decompositions, Machine learning, Preprocessing, fMRI & imaging, Single-unit activity, calcium imaging
Keywords: Motivation, Reward, Olfactory cortex
MeSH: Neurons*, Prefrontal Cortex*, Reward*, Animals, Male, Mice, Mice, Inbred C57BL, Odorants (* major topic)
Topic: Neural dynamics and brain function (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Funding: U.S. Department of Health & Human Services | National Institutes of Health (R01MH116937, MH106435, RF1 DA056403, R01MH110594); NIDA NIH HHS (RF1 DA056403); Gatsby Charitable Foundation; Simons Foundation; National Science Foundation (2427124); James S. McDonnell Foundation (220020466); McKnight Foundation; NIMH NIH HHS (R01 MH110594, P50 MH106435, R01 MH116937); U.S. Department of Health & Human Services | National Institutes of Health (NIH) (R01MH110594, MH106435, R01MH116937, RF1 DA056403)
Citations: cited by 1 paper (Europe PMC); 91 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repositories

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Zenodo 20477351

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State: the link answers, verified on 27 September 2026
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Size: 4 files
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Found in: the references
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
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At the source:

Zenodo 20479276

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Zenodo 20480778

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jjbussell/Bussell2026InfoValue

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 1f3cffda257c23ff315d6a410072af60994392bd, 19 August 2026
Languages: MATLAB (70), C++ (1), C/C++ (1), Python (1), Shell (1)
Size: 90 files, 74 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README, 1 notebook
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Statistics and Machine Learning Toolbox (12 files), Image Processing Toolbox (2 files), Violinplot-Matlab (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
75 files
At the source: github.com/jjbussell/Bussell2026InfoValue

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Data

Datasets cited

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Versions

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Version 2, 28 September 2026

  • Publisher: n/a → Nature Portfolio

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 3 keywords, 8 MeSH terms, 9 funders, 80 references.

Cite

This paper

Bussell, J. J., Badman, R. P., Márton, D., Bromberg-Martin, E. S., Abbott, L. F., Rajan, K., & Axel, R. (2026). Representations of the intrinsic value of information in mouse orbitofrontal cortex. Nature neuroscience, 29(9), 2261-2272. https://doi.org/10.1038/s41593-026-02377-y

BibTeX

@article{bussell2026representations,
author = {Bussell, Jennifer J and Badman, Ryan P and Márton, David and Bromberg-Martin, Ethan S and Abbott, L F and Rajan, Kanaka and Axel, Richard},
title = {{Representations of the intrinsic value of information in mouse orbitofrontal cortex}},
journal = {Nature neuroscience},
year = {2026},
month = jul,
volume = {29},
number = {9},
pages = {2261--2272},
publisher = {Nature Portfolio},
issn = {1097-6256},
doi = {10.1038/s41593-026-02377-y},
url = {https://doi.org/10.1038/s41593-026-02377-y},
pmid = {42533133},
pmcid = {PMC13533842}
}

RIS

TY - JOUR
AU - Bussell, Jennifer J
AU - Badman, Ryan P
AU - Márton, David
AU - Bromberg-Martin, Ethan S
AU - Abbott, L F
AU - Rajan, Kanaka
AU - Axel, Richard
TI - Representations of the intrinsic value of information in mouse orbitofrontal cortex
T2 - Nature neuroscience
J2 - Nat Neurosci
PY - 2026
DA - 2026/07/30
VL - 29
IS - 9
SP - 2261
EP - 2272
SN - 1097-6256
PB - Nature Portfolio
DO - 10.1038/s41593-026-02377-y
UR - https://doi.org/10.1038/s41593-026-02377-y
LA - en
ER -

CSL-JSON

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"id": "10.1038/s41593-026-02377-y",
"type": "article-journal",
"title": "Representations of the intrinsic value of information in mouse orbitofrontal cortex",
"container-title": "Nature neuroscience",
"author": [
{
"family": "Bussell",
"given": "Jennifer J"
},
{
"family": "Badman",
"given": "Ryan P"
},
{
"family": "Márton",
"given": "David"
},
{
"family": "Bromberg-Martin",
"given": "Ethan S"
},
{
"family": "Abbott",
"given": "L F"
},
{
"family": "Rajan",
"given": "Kanaka"
},
{
"family": "Axel",
"given": "Richard"
}
],
"container-title-short": "Nat Neurosci",
"volume": "29",
"issue": "9",
"page": "2261-2272",
"DOI": "10.1038/s41593-026-02377-y",
"PMID": "42533133",
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"publisher": "Nature Portfolio",
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"language": "en",
"issued": {
"date-parts": [
[
2026,
7,
30
]
]
}
}

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