THE AUDITORY MODELING TOOLBOX
DATA_HEERINGA2024
Single-unit responses from the auditory nerve of gerbils
Usage:
data = data_heeringa2024(flag); data = data_heeringa2024(flag, animalID); data = data_heeringa2024(.., 'unit', unit);
Description:
data_heeringa2024(flag) plots various figures from Heeringa (20204) or displays tables.
data = data_heeringa2024(flag) returns the corresponding data to a variable.
The following flags can be provided:
| 'list' | Returns a cell array with available animal IDs. The animal ID can be used as animalID to retrieve data and info and plot specific figures. |
| 'info' | Returns the information about an animal. Provide animalID to specify the animal (default: G220922). For more details, see exp.info in https://datadryad.org/stash/downloads/file_stream/3070542. |
| 'data' | Returns the responses from an animal. Provide animalID to specify the animal (default: G220922). The output data is structure containing all the data and metadata structured by units and recording types. Note that data of some animals are stored in multiple batches to keep the file sizes below 1 GB. All data from all batches are returned. For more details, see exp.data in https://datadryad.org/stash/downloads/file_stream/3070542. |
| 'fig3' | Reproduce Fig. 3: Plot the animal's hearing sensitivity as derived from the ABR to chirps as a function of the animal's age in months. Males and females are plotted separately. |
| 'fig4' | Reproduce Fig. 4: Plot the waveform shapes of a single unit. Default is the animal G220922 and unit 12 (3p_607). |
| 'fig5a' | Reproduce Fig. 5a: Plot all rate-level functions from an animal. Default is the animal G220922. |
| 'fig5b' | Reproduce Fig. 5b: Plot a PSTH from the animal G220908 and unit 23 (3p_181) at the test level of 20 dB above threshold. |
| 'fig6' | Reproduce Fig. 6: Plot BF vs threshold (Fig. 6a), BF distribution in young- adult gerbils (Fig. 6b), BF vs spontaneous rate (Fig. 6c) and BF vs vector strength to pure tones at BF (Fig. 6d) based on the full dataset. |
| 'fig7' | Reproduce Fig. 7: Fig. 7a: Characteristic frequencies as a function of the fibre’s BF and as a histogram. Fig. 7b: Click latencies as a function of the BF with their histogram. Fig. 7c: Spontaneous rates (SR) as a function of fibre's BF. Fig. 7d, 7e, and 7f: Thresholds for the complex stimuli recordings NOISE, SPS, and CVC, respectively. |
| 'tab1' | Returns the Tab. 1 from Heeringa (20204). |
| 'summary' | Returns a summary table with the metadata of the dataset. |
data_heeringa2024(.., 'unit', unit) plots and/or provides data for a specific unit number. Default is unit 1, except for Fig. 4, where default is unit 12 to be consistent with Heeringa (2004).
Examples:
To display Fig. 3 use :
data_heeringa2024('fig3');
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To display Fig. 4 use :
data_heeringa2024('fig4');
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To display Fig. 5a use :
data_heeringa2024('fig5a');
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To display Fig. 5b use :
data_heeringa2024('fig5b');
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To display Fig. 6 use :
data_heeringa2024('fig6');
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To display Fig. 7 use :
data_heeringa2024('fig7');
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To display Tab. 1 use :
data_heeringa2024('tab1');
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This code produces the following output::
Young_adult Middle_aged Quiet_aged
___________ ___________ __________
Total number of animals 60 13 31
Number of female animals 32 7 11
Age in months (mean) 5.5468 22.49 38.328
Age in months (std. dev) 2.0326 6.2223 1.7006
Age in months (min) 2.7288 12.559 36.033
Age in months (max) 11.408 33.173 41.721
ABR threshold in dB SPL (mean) 18.1 34.167 49.032
ABR threshold in dB SPL (std. dev.) 5.3347 10.188 18.001
ABR threshold in dB SPL (min) 10 20 20
ABR threshold in dB SPL (max) 30 50 85
Weight in grams (mean) 74.607 83.354 86.413
Weight in grams (std. dev) 11.07 12.669 11.6
Weight in grams (min) 51.2 66.8 60
Weight in grams (max) 100 103 120
Total number of single units 759 87 314
Range of best frequency in Hz (min) 428 350 620
Range of best frequency in Hz (max) 15825 15091 15762
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To display the summary of all data use :
data_heeringa2024('summary');
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This code produces the following output:: animalID age_days sex ABR_threshold n_units BF_range n_BF n_CF n_PH n_CLICK n_RLF n_SR n_NOISE n_SPS n_CVC _________ ________ ___ _____________ _______ _______________ ____ ____ ____ _______ _____ ____ _______ _____ _____ 'G191008' 125 'M' 15 5 '8606 - 13906' 5 0 0 1 5 5 0 0 3 'G191022' 128 'F' 20 7 '1239 - 9300' 7 0 0 1 6 4 0 0 4 'G191115' 163 'M' 15 19 '1830 - 11474' 19 0 3 5 14 11 0 0 11 'G191128' 176 'M' 25 9 '880 - 15531' 9 0 2 4 9 5 0 0 7 'G191217' 184 'F' 15 2 '1478 - 2243' 2 0 0 0 2 1 0 0 2 'G191219' 182 'F' 10 2 '1548 - 3078' 2 0 0 0 1 0 0 0 0 'G200213' 1259 'M' 30 18 '744 - 9432' 18 0 0 0 18 6 0 0 10 'G200225' 1260 'F' 35 19 '652 - 8783' 19 0 5 5 16 6 0 0 10 'G200306' 125 'F' 20 12 '4805 - 9146' 12 0 0 6 8 7 0 0 5 'G200528' 116 'F' 10 16 '1973 - 7631' 16 0 0 7 16 13 0 0 12 'G200616' 135 'M' 15 11 '657 - 11402' 11 0 1 3 7 2 0 0 6 'G200623' 142 'M' 10 17 '852 - 11278' 17 0 3 4 16 4 0 0 11 'G201001' 1157 'M' 45 39 '640 - 12523' 39 0 12 16 39 18 0 0 31 'G201103' 98 'M' 15 24 '2531 - 13715' 24 0 2 7 21 7 0 0 2 'G201112' 107 'F' 15 28 '3584 - 14398' 28 0 1 8 24 4 0 0 0 'G201208' 1145 'F' 30 23 '2019 - 7617' 23 0 2 6 19 3 0 0 0 'G201210' 132 'F' 15 14 '5924 - 14512' 14 0 2 6 13 6 0 0 0 'G201215' 137 'M' 15 19 '1575 - 12747' 19 0 0 5 17 4 0 0 0 'G201217' 1121 'M' 30 2 '7963 - 8193' 2 0 1 1 2 1 0 0 0 'G201222' 144 'M' 10 9 '1918 - 14800' 9 0 0 1 6 0 0 0 3 'G211118' 1116 'M' 20 14 '1972 - 10154' 14 0 2 6 13 6 0 0 9 'G211221' 1150 'M' 50 19 '785 - 7192' 19 0 7 14 16 14 0 0 4 'G220201' 157 'F' 15 21 '576 - 13791' 21 0 0 6 20 8 0 0 0 'G220222' 178 'F' 15 8 '480 - 13263' 8 0 1 2 7 2 0 0 0 'G220301' 185 'F' 10 11 '2830 - 8413' 11 0 0 5 11 5 0 0 0 'G220331' 1178 'M' 80 11 '2614 - 5835' 11 0 6 7 9 7 0 0 0 'G220407' 1185 'F' 75 1 '12882 - 12882' 1 0 0 1 1 1 0 0 0 'G220602' 1255 'M' 75 4 '1108 - 3097' 4 0 2 2 4 2 0 0 0 'G220609' 1257 'M' 40 12 '847 - 8253' 12 0 0 6 11 6 0 0 5 'G220726' 1113 'F' 25 7 '4316 - 15762' 7 0 0 1 7 2 0 0 0 'G220901' 105 'F' 15 26 '1209 - 13416' 26 1 2 8 20 11 0 0 0 'G220908' 112 'F' 15 30 '545 - 12689' 30 0 3 5 26 10 0 0 0 'G220922' 126 'M' 15 18 '3138 - 11141' 18 0 0 4 13 3 0 0 0 'G221006' 1185 'M' 85 1 '4839 - 4839' 1 0 0 0 1 1 0 0 0 'G221013' 1111 'F' 40 1 '11012 - 11012' 1 0 0 1 1 0 0 0 0 'G221110' 175 'M' 10 7 '8168 - 15825' 7 0 0 0 4 3 0 0 0 'G200901' 787 'F' 30 14 '1099 - 12326' 14 0 0 9 14 0 0 0 0 'G180205' 183 'M' 20 13 '1359 - 11490' 12 0 5 2 9 0 0 0 0 'G190118' 1200 'M' 40 5 '749 - 10213' 5 1 1 0 4 0 3 0 0 'G190129' 1126 'F' 60 12 '868 - 10623' 12 3 3 3 10 0 6 0 0 'G190603' 125 'M' 25 25 '926 - 14994' 25 4 13 0 24 0 18 0 0 'G190611' 1163 'F' 60 2 '6552 - 7401' 2 0 1 1 2 0 2 0 0 'G190613' 135 'M' 20 1 '7406 - 7406' 1 0 0 0 1 0 1 0 0 'G190617' 139 'M' 25 29 '2395 - 12801' 29 0 9 0 26 0 16 0 0 'G190704' 156 'F' 25 21 '820 - 12725' 21 0 5 0 21 0 0 0 0 'G170523' 228 'F' 20 6 '1188 - 12121' 6 1 4 0 5 0 0 2 0 'G170712' 278 'F' NaN 2 '645 - 9777' 2 0 0 0 2 0 0 0 0 'G171211' 219 'M' 25 10 '1596 - 7722' 10 0 9 5 10 0 0 2 0 'G180626' 723 'F' 40 8 '1133 - 7922' 8 0 3 0 8 0 0 0 0 'G180710' 230 'M' 20 15 '828 - 3315' 15 0 2 0 15 0 0 5 0 'G180717' 237 'F' 30 10 '872 - 11863' 10 0 0 0 10 0 0 0 0 'G190108' 1009 'F' 45 14 '967 - 10359' 14 4 2 4 12 0 7 0 0 'G190411' 144 'F' 15 35 '471 - 11962' 35 1 1 3 35 0 6 0 0 'G190507' 228 'F' 15 7 '1320 - 6166' 7 0 0 0 6 0 0 0 0 'G190801' 1154 'F' 60 10 '683 - 4101' 10 4 4 2 10 0 6 0 0 'G190806' 1132 'F' 35 4 '732 - 1233' 4 2 3 2 4 0 3 0 0 'G191017' 1151 'M' 50 6 '769 - 4895' 6 2 2 6 6 0 0 0 0 'G190903' 1096 'M' 60 10 '4940 - 12187' 10 1 1 3 10 0 0 0 0 'G190912' 1105 'M' 35 18 '871 - 12973' 18 2 4 12 18 0 0 0 0 'G190920' 1113 'M' 35 1 '9359 - 9359' 1 0 0 1 1 0 0 0 0 'G180118' 540 'M' 25 6 '6128 - 11587' 6 0 0 0 4 0 0 0 0 'G171214' 1196 'F' 65 3 '638 - 1715' 3 0 2 0 2 0 0 0 0 'G150717' 83 'M' 10 1 '1661 - 1661' 1 1 1 1 1 0 0 0 0 'G150730' 85 'M' 15 13 '616 - 2613' 12 3 5 6 7 0 0 0 0 'G150805' 83 'F' 15 4 '529 - 1703' 4 1 1 1 2 0 0 0 0 'G150921' 93 'M' NaN 6 '862 - 2224' 6 3 1 2 2 0 0 0 0 'G150922' 83 'F' NaN 21 '526 - 12359' 20 13 13 0 17 0 0 0 0 'G150929' 89 'F' NaN 2 '5253 - 5384' 2 1 1 0 1 0 0 0 0 'G151001' 122 'F' NaN 24 '1002 - 6126' 24 15 17 0 21 0 0 0 0 'G151104' 102 'M' NaN 9 '1292 - 11149' 9 3 0 1 7 0 0 0 0 'G151110' 129 'M' NaN 2 '700 - 946' 2 1 1 1 1 0 0 0 0 'G151126' 145 'M' NaN 25 '541 - 3429' 23 7 15 7 11 0 0 0 0 'G151203' 152 'F' NaN 22 '468 - 12301' 21 7 14 12 13 0 0 0 0 'G151210' 829 'M' NaN 11 '1212 - 4647' 11 6 11 5 11 0 0 0 0 'G160322' 347 'M' 30 2 '4843 - 8474' 2 0 1 0 1 0 0 0 0 'G160412' 191 'F' 20 3 '7343 - 7352' 3 1 0 1 1 0 0 0 0 'G160419' 198 'F' 20 9 '5449 - 8648' 9 6 3 3 9 0 0 0 0 'G160426' 382 'M' 20 1 '15017 - 15017' 1 0 0 0 0 0 0 0 0 'G160504' 213 'F' 20 13 '468 - 8511' 13 7 10 5 12 0 11 0 0 'G160518' 805 'F' 40 3 '508 - 2023' 3 2 3 0 3 0 2 0 0 'G160524' 410 'F' 20 5 '2091 - 13433' 5 0 1 1 2 0 0 0 0 'G160531' 332 'M' NaN 8 '2441 - 8033' 8 1 2 1 3 0 3 0 0 'G160609' 249 'F' 15 2 '1514 - 2669' 2 0 2 0 2 0 0 0 0 'G160727' 203 'M' 25 1 '14998 - 14998' 1 0 0 0 1 0 0 0 0 'G160803' 698 'F' 45 5 '1746 - 1811' 5 1 3 0 3 0 4 0 0 'G160817' 897 'M' 35 5 '7151 - 15091' 5 3 0 0 3 0 3 0 0 'G160901' 728 'M' 50 10 '350 - 6011' 10 4 6 0 6 0 7 0 0 'G161110' 140 'M' 20 7 '2341 - 12125' 7 1 1 0 2 0 2 0 0 'G170425' 253 'F' 25 9 '445 - 4574' 9 0 7 0 8 0 0 1 0 'G170508' 1161 'M' 65 3 '1301 - 4423' 2 0 1 0 1 0 0 0 0 'G170512' 264 'F' 20 26 '428 - 15824' 25 3 13 0 13 0 15 12 0 'G171023' 1145 'M' 75 12 '846 - 5182' 12 1 8 4 4 0 10 0 0 'G180406' 1178 'M' 30 22 '699 - 14271' 22 0 3 0 14 0 13 0 0 'G170517' 573 'F' 35 4 '9260 - 9746' 4 0 0 0 2 0 0 0 0 'G171221' 512 'M' 25 1 '8894 - 8894' 1 0 0 0 1 0 0 0 0 'G170808' 205 'M' 20 2 '8546 - 8972' 2 0 0 0 1 0 0 0 0 'G190730' 1212 'M' 50 3 '5129 - 6136' 3 0 0 0 3 0 0 0 0 'G190515' 273 'F' 25 13 '921 - 10767' 13 2 1 3 13 0 0 0 0 'G171204' 257 'M' 25 2 '9455 - 11726' 2 0 0 1 2 0 0 0 0 'G190326' 1269 'M' 65 12 '620 - 8030' 12 0 1 1 11 0 5 0 0 'G230511' 1146 'M' 35 9 '5382 - 9845' 9 0 0 3 9 2 0 0 0 'G230907' 1101 'F' 40 11 '3209 - 15435' 11 0 0 3 8 6 0 0 0 'G231218' 187 'F' 20 27 '597 - 15509' 27 0 0 1 17 3 0 0 0 'G240111' 211 'F' 20 17 '808 - 5922' 17 0 4 5 11 4 0 0 0 |
References:
A. N. Heeringa, F. Teske, G. Ashida, and C. Köppl. Cochlear aging disrupts the correlation between spontaneous rate and sound-level coding in auditory nerve fibers. Journal of Neurophysiology, 130(3):736--750, 2023. PMID: 37584075. [ DOI ]
A. N. Heeringa and C. Köppl. Auditory nerve fiber discrimination and representation of naturally-spoken vowels in noise. eNeuro, 9(1), 2022. [ DOI ]
F. Steenken, A. N. Heeringa, R. Beutelmann, L. Zhang, S. Bovee, G. M. Klump, and C. Köppl. Age-related decline in cochlear ribbon synapses and its relation to different metrics of auditory-nerve activity. Neurobiology of Aging, 108:133--145, 2021. [ DOI ]
A. N. Heeringa, L. Zhang, G. Ashida, R. Beutelmann, F. Steenken, and C. Köppl. Temporal coding of single auditory nerve fibers is not degraded in aging gerbils. Journal of Neuroscience, 40(2):343--354, 2020. [ DOI ]
A. N. Heeringa, C. Jüchter, R. Beutelmann, G. M. Klump, and C. Köppl. Altered neural encoding of vowels in noise does not affect behavioral vowel discrimination in gerbils with age-related hearing loss. Frontiers in Neuroscience, 17, 2023. [ DOI ]
F. Steenken, H. Oetjen, R. Beutelmann, L. H. Carney, C. Koeppl, and G. M. Klump. Neural processing and perception of schroeder-phase harmonic tone complexes in the gerbil: Relating single-unit neurophysiology to behavior. European Journal of Neuroscience, 56(3):4060--4085, 2022. [ DOI ]
A. Heeringa. Single-unit auditory nerve fibre responses of young-adult and aging gerbils, 2024. [ DOI ]
A. N. Heeringa. Single-unit data for sensory neuroscience: Responses from the auditory nerve of young-adult and aging gerbils. Scientific Data, 11:411, Apr. 2024. [ DOI ]
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