Self-organization of songbird neural sequences during social isolation

  1. Emily L Mackevicius
  2. Shijie Gu
  3. Natalia I Denisenko
  4. Michale S Fee  Is a corresponding author
  1. McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, MIT, United States
3 figures, 1 table and 1 additional file

Figures

Figure 1 with 10 supplements
Sequences in isolated birds.

(A) Diagram of HVC maturation. In typically tutored birds, HVC sequences appear to grow and differentiate over time. (B) Example neural sequences recorded in a singing isolated bird (older juvenile, …

Figure 1—figure supplement 1
HVC sequences exist even in young isolated birds.

(A) Example HVC sequences recorded in a young isolated bird (59 dph) (B–F) Sequence properties as a function of age in seven juvenile isolated birds (five birds recorded prior to the closing of the …

Figure 1—figure supplement 2
Estimating the number of significant sequences in each dataset.

(A) Reconstruction cost (red) and correlation cost (blue) as a function of λ (with K=10, L=0.5s) for eight datasets (pre-tutoring data from eight different birds). The crossover point, λ0, is …

Figure 1—figure supplement 3
Enlarged data, bird 6961.

Enlarged panel showing spectrogram, neural data, and seqNMF factorization for 6 s of pre-tutoring data.

Figure 1—figure supplement 4
Enlarged data, bird 6991.

Enlarged panel showing spectrogram, neural data, and seqNMF factorization for 6 s of pre-tutoring data.

Figure 1—figure supplement 5
Enlarged data, bird 7030.

Enlarged panel showing spectrogram, neural data, and seqNMF factorization for 6 s of pre-tutoring data.

Figure 1—figure supplement 6
Enlarged data, bird 7187.

Enlarged panel showing spectrogram, neural data, and seqNMF factorization for 6 s of pre-tutoring data.

Figure 1—figure supplement 7
Enlarged data, bird 6938.

Enlarged panel showing spectrogram, neural data, and seqNMF factorization for 6 s of pre-tutoring data.

Figure 1—figure supplement 8
Enlarged data, bird 6992.

Enlarged panel showing spectrogram, neural data, and seqNMF factorization for 6 s of pre-tutoring data.

Figure 1—figure supplement 9
Enlarged data, bird 6962.

Enlarged panel showing spectrogram, neural data, and seqNMF factorization for 6 s of pre-tutoring data.

Figure 1—figure supplement 10
Enlarged data, bird 6922.

Enlarged panel showing spectrogram, neural data, and seqNMF factorization for 6 s of pre-tutoring data.

Figure 2 with 4 supplements
Relation between HVC sequence maturity and subsequent song learning.

(A) Example spectrograms for two non-learner birds, prior to tutoring and several weeks later (at least 77dph). (B) Example spectrograms for two learners, prior to tutoring, shortly after tutoring, …

Figure 2—figure supplement 1
Elaborations on tutor match, bird 6938.

Song spectrograms at different stages of development, and comparison to tutor song spectrogram. Colored bars match elements of the imitation to tutor song syllables.

Figure 2—figure supplement 2
Elaborations on tutor match, bird 6992.

Song spectrograms at different stages of development, and comparison to tutor song spectrogram. Colored bars match elements of the imitation to tutor song syllables.

Figure 2—figure supplement 3
Elaborations on tutor match, bird 6962.

Song spectrograms at different stages of development, and comparison to tutor song spectrogram. Colored bars match elements of the imitation to tutor song syllables.

Figure 2—figure supplement 4
Elaborations on tutor match, bird 6922.

Song spectrograms at different stages of development, and comparison to tutor song spectrogram.Colored bars match elements of the imitation to tutor song syllables.

Tracking HVC sequences as isolated birds rapidly learn a new syllable.

(A) Neurons detected before (left) and after (right) tutoring shown in grayscale (CNMF_E algorithm). Colored contours indicate locations of neurons tracked across five days, from blue to red (B) …

Tables

Key resources table


Reagent type (species) or resource
DesignationSource or referenceIdentifiersAdditional information
Software, algorithm
seqNMFMackevicius et al., 2019github.com/FeeLab/seqNMFSequence detection
Software, algorithm
CNMF_EZhou et al., 2018github.com/zhoupc/CNMF_ECell extraction
Software, algorithm

STATGu et al., 2023https://github.com/shijiegu/STATTracking neurons across days
Software, algorithm

ChronuxMitra and Bokil, 2007chronux.org/Spectrogram computation
Software, algorithm
SAPTchernichovski et al., 2000soundanalysispro.comSound analysis
Software, algorithm
SIMandelblat-Cerf and Fee, 2014https://doi.org/10.1371/journal.pone.0096484Song imitation
Software, algorithm

MATLABMathWorksmathworks.com/products/matlabProgramming language
Biological sample (Taeniopygia guttata)
Zebra finchesMIT animal facilityTaeniopygia guttata
Strain, strain background
(adeno-associated virus)
AAV9.CAG.GCaMP6f.
WPRE.SV40
Chen et al., 2013Addgene viral prep # 100836-AAV9,
http://n2t.net/addgene:100836,
RRID:Addgene_100836

Commercial assay or kit
Miniature microscopeInscopixhttps://www.inscopix.com/nvista

Additional files

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