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In Vivo Visualization of Spontaneous Activity in Neonatal Mouse Sensory Cortex at a Single-Neuron Resolution

Published: November 21, 2023 doi: 10.3791/65899
* These authors contributed equally


Primary sensory areas in the neocortex exhibit unique spontaneous activities during development. This article describes how to visualize individual neuron activities and primary sensory areas to analyze area-specific synchronous activities in neonatal mice in vivo.


The mammalian brain undergoes dynamic developmental changes at both the cellular and circuit levels throughout prenatal and postnatal periods. Following the discovery of numerous genes contributing to these developmental changes, it is now known that neuronal activity also substantially modulates these processes. In the developing cerebral cortex, neurons exhibit synchronized activity patterns that are specialized to each primary sensory area. These patterns markedly differ from those observed in the mature cortex, emphasizing their role in regulating area-specific developmental processes. Deficiencies in neuronal activity during development can lead to various brain diseases. These findings highlight the need to examine the regulatory mechanisms underlying activity patterns in neuronal development. This paper summarizes a series of protocols to visualize primary sensory areas and neuronal activity in neonatal mice, to image the activity of individual neurons within the cortical subfields using two-photon microscopy in vivo, and to analyze subfield-related activity correlations. We show representative results of patchwork-like synchronous activity within individual barrels in the somatosensory cortex. We also discuss various potential applications and some limitations of this protocol.


The cerebral cortex contains several sensory areas with distinct functions. The areas receive inputs originating from their corresponding sensory organs, mostly conveyed through the spinal cord or brainstem and relayed via the thalamus1,2. Notably, neurons in each primary sensory area exhibit uniquely synchronized activity during early developmental stages, which also originate from sensory organs or the lower nervous centers, but essentially differ from the activities observed in the mature cortex3.

In neonatal rodents, for example, the primary visual area (V1) displays wave-like activity, which originates in the retina (retinal wave) and propagates through the entire visual pathway while conserving retinotopy4. The primary auditory area (A1) exhibits synchronous activity organized in band-shaped subregions that correspond to the isofrequency bands in the mature brain. The activity emanates from the cochlea's inner hair cells5,6. The barrel cortex in the primary somatosensory area (S1) shows a patchwork-like activity pattern in which layer 4 neurons within individual barrels, namely, neurons responsive to individual whiskers, are synchronously activated7. Although proposed to originate from the trigeminal ganglion, the source of the activity remains unknown7. Consequently, neonatal activity patterns are specialized both within each primary sensory area and within intra-areal subfields. The simultaneous visualization of neuronal activity and structure of primary sensory areas may facilitate an inquiry into the contribution of these activity patterns to the development of sensory systems.

In this article, we summarized a series of protocols: (1) to visualize individual neuronal activities using sparse labeling of GCaMP and primary sensory areas using TCA-RFP mice that express red fluorescent protein in thalamocortical axons7, (2) to image single cell-level activity in neonatal mice using two-photon microscopy in vivo, and (3) to analyze the activity correlations within S1 barrel cortex. The representative results show patchwork-like synchronized activity within individual barrels of a postnatal day (P)6 mouse. Despite some limitations, this technique can be used for chronic imaging, wide-field imaging across multiple sensory areas, and various manipulation experiments. The multifaceted analysis of neuronal activity during development will enrich our comprehension of brain circuit formation mechanisms.

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All the experiments were conducted in accordance with the guidelines for animal experimentation of Kumamoto University and the National Institute of Genetics and approved by the animal experimentation committees.

1. In utero electroporation (IUE)

  1. Mate male TCA-RFP mice of ICR background with female wild-type ICR mice. Observe the vaginal plug to check for mating early morning of the next day. Observe the abdomen to check for pregnancy 2 weeks later.
  2. Prepare plasmid solution containing 5 ng/µL TRE-nCre, 1 µg/µL CAG-loxP-stop-loxP-GCaMP6s-ires-tTA-WPRE, and 0.02 % Trypan Blue in ddH2O to sparsely label neurons by GCaMP using the Supernova system8.
  3. Prepare an analgesic solution by diluting 50 mg/mL carprofen (100x) to a final concentration of 0.5 mg/mL. Keep it at room temperature.
  4. At embryonic day (E)14, perform IUE as follows. The IUE methods are essentially the same as previous reports9,10,11.
    1. Wipe the lab bench with 70% ethanol. Sterilize all surgical instruments with 70% ethanol. Wear a mask and a lab coat to reduce the risk of infection to the mouse.
    2. Prepare glass micropipettes using a micropipette puller. Take the plasmid mixture solution into the glass micropipette using an aspirator tube.
    3. Anesthetize the pregnant mice at E14 with sodium pentobarbital intraperitoneal injection (50 mg/kg body weight). Keep the mice anesthetized during the procedure with isoflurane (0.8%-1.2% in air). Pinch the toe to ensure that the anesthesia is deep enough. Use eye drops to prevent eye dryness.
    4. Sterilize the abdominal area with 70% ethanol and make a midline incision. Place a saline-moistened non-woven fabric around the incision. Expose the uterus onto the fabric.
    5. Repeat dripping warm saline onto the uterus to prevent it from drying or cooling until abdomen closure (Step 1.4.8).
    6. Inject the plasmid solution into one side of the lateral ventricle of embryos one by one using a micropipette and an aspirator tube.
    7. Use a forceps-type electrode to pinch the embryo heads and deliver square electric pulses (40 V, 50 ms) five times at 1 s intervals using an electroporator.
    8. Return the uterus to the abdominal cavity. Apply ~3 mL of warm saline into the cavity. Suture the peritoneal membrane and the abdominal skin. Administer the analgesic solution at 10 µL/g weight (carprofen at 5 µg/g weight) under the skin at the back of the neck.
  5. Place the mouse on a heater (37 °C) to recover from anesthesia. Lay the mouse on its belly to prevent its tongue and saliva from choking the throat. Keep the mouse apart from other mice and monitor it until it recovers to move normally. Return the mouse to the cage.
  6. After birth, perform genotyping to check for RFP allele, and euthanize the pups without the allele. This step is recommended, especially if imaging is done during the second postnatal week when the TCA-RFP signal is weak and difficult to check at step 2.2.7.

2. Cranial window surgery

  1. Prepare the cortex buffer containing 125 mM NaCl, 5 mM KCl, 10 mM glucose, 10 mM HEPES, 2 mM CaCl2, and 2 mM MgSO4 in ddH2O (pH adjusted to 7.4 with 1 M NaOH)12 before the day of surgery. Sterile the buffer using a vacuum filter.
    NOTE: The buffer can be kept at 4 °C for up to 3 months. The required volume is 5-10 mL per pup.
  2. Perform the following steps at P3-12. Also see the previous reports that have described this procedure13,14.
    1. Mix 50 mg of agarose with 5 mL of cortex buffer and completely dissolve the agarose by heating. Take some of the solution into a 1.5 mL tube and keep it at 42 °C.
    2. Take some cortex buffer into a 50 mL conical tube and keep it at room temperature. Take some saline into a container (e.g., a cap of a 50 mL conical tube) and keep it at room temperature.
    3. Prepare an analgesic solution by diluting 50 mg/mL carprofen for 100x to be 0.5 mg/mL. Take some of the solution in a 1.5 mL tube and keep it at room temperature.
    4. Sterilize all surgical instruments with 70% ethanol.
    5. Place a pup in an acrylic anesthetic container and anesthetize by putting an isoflurane-soaked paper in the container. Pay attention to the pup and take it out when its breathing slightly slows down.
      NOTE: If the anesthesia is prolonged, the pup's breathing may cease for a few seconds. Even if the pup's breathing is resumed, prolonged anesthesia may decrease the pup's cerebral blood flow and cause irreversible brain damage.
    6. Make a scalp incision to expose the skull of the plasmid-introduced side. Place the pup onto the heating pad (35 °C) under a fluorescence stereo microscope. Always keep the pup anesthetized with isoflurane (1.5%-2.5% in air).
    7. Select the pups expressing TCA-RFP and GCaMP by observing the fluorescence through the skull. Euthanize the pups that do not express both.
    8. Remove the scalp above the cerebral hemispheres as widely as possible carefully so as not to cause bleeding. Rub the skull with a saline-soaked cotton swab to remove connective tissue.
    9. After the skull dries, adhere the incised scalp surface to the skull with a tissue adhesive.
    10. Transfer the pup onto a 37 °C heating pad to recover from anesthesia. Wait for at least 15 min to let the adhesive solidify.
      NOTE: Pause for up to 1 h before moving on to the next step. Prepare other pups in a similar manner if needed during this time.
    11. Anesthetize the pup with isoflurane. Place the pup onto the heating pad (35 °C) under a fluorescence stereo microscope while anesthetized (1.5%-2.5% isoflurane in air).
    12. Mark the GCaMP-expressing location on the skull with a permanent marker. Apply cortex buffer onto the location.
    13. Insert the corner of a razor blade into the skull. Push the blade slowly to shave off the skull and make a hole. Pinch off the cracked skull with tweezers and remove it.
    14. Check that the cranial hole is successfully made by observing blood vessels in the hole. If bleeding occurs, quickly rinse the hole with cortex buffer using a micropipette. Repeat rinsing until the bleeding stops completely.
    15. Apply a drop of cortex buffer to the cranial hole and place in a 3-mm-diameter round coverglass over the hole. Wipe away the excess buffer with non-woven fabric. Wait until the area around the glass dries.
    16. Apply warm agarose solution around the glass edge using a micropipette. Because too much agarose may reduce the fluorescent signals, remove the excess solution under the glass by gently pushing the glass from above.
    17. Remove the agarose on the glass or distant from the glass edge using tweezers. Leave agarose only around the outer glass perimeter.
    18. Wait until the agarose solidifies. If agarose shrinkage makes a space under the glass, add agarose solution from the side to cover the entire glass edge. Remove any liquid from the skull surface with non-woven fabric.
    19. Mix acrylic resin powder and liquid in a rubber container. Aspirate the mixture with a micropipette and pour it to cover the agarose surrounding the glass edge with resin.
      NOTE: Because the resin solidifies soon after mixing the powder and liquid, they need to be mixed repeatedly before applying. The amounts needed in each mixing are ~500 µL for liquid and ~0.15 g for powder.
    20. Fix a titanium bar with resin on the contralateral hemisphere. Keep the bar angle parallel to the cover glass. Fix the entire skull surface with resin.
    21. Administer the analgesic solution at 10 µL/g weight (carprofen at 5 µg/g weight) under the skin at the back of the neck. Return the pup to a 37 °C heating pad for anesthesia recovery. Wait for >60 min for resin solidification before imaging.
      ​NOTE: Pause for 1-5 h before imaging. Perform surgery on other pups in a similar manner during this time.

3. Two-photon calcium imaging

  1. Attach a two-axis goniometer with a titanium plate to a stage plate with XY positioning beneath the microscope. Set up a heating pad (35 °C) on the stage.
  2. Turn on the scanning software with the following conditions: Pixels, 512 x 512; Bidirectional, ON; Averaging, none; imaging area, 600 x 600 µm with a 20x objective. Set the settings so that the scan rate is faster than 1 Hz.
  3. Place the pup on the heating pad, and fix the head-mount titanium bar to the titanium plate with screws. Keep the pup anesthetized by placing a tube port for isoflurane (1.5-2.0% in air).
  4. Adjust the window angle horizontally by the goniometer. Turn on the backlight and observe the brain surface with a 5x objective lens, and select the imaging area by XY positioning.
  5. Put eye drops on the cranial window. Switch the objective to a 20x water-immersion lens. Observe the cortical surface to confirm that blood flow is seen on the brain surface.
  6. Turn off the backlight and scan the brain surface using one-photon mode. Increase the laser power to make the green autofluorescence of the glass and the brain surface visible.
  7. Lower the isoflurane concentration to 1.0%-1.5%. Cover the microscope to avoid light leaks. Switch the scanning software to two-photon mode.
  8. Adjust the laser power and detector gain appropriate for scanning GCaMP and RFP signals. Find the depth where TCA-RFP signals are seen. Make sure that the depth is layer 4, ~300 µm lower than the brain surface at P6. Select the imaging area where many GCaMP-expressing neurons are seen.
  9. Start timelapse imaging of GCaMP and RFP signals. If two-channel simultaneous scanning is inapplicable, capture GCaMP and TCA-RFP images before the imaging.
  10. Stop isoflurane to weaken the anesthesia and observe spontaneous activities for ~20 min. When the pup starts moving, stop imaging and anesthetize the pup again (induce with 2% isoflurane, and then lower to 1.2%-1.5% in air).
  11. After the pup stops moving, repeat the imaging from Step 3.9. Change the imaging area if needed.
  12. Fix the brain by transcardial perfusion of saline and 4% PFA, followed by post-fixation in 4% PFA overnight to prepare tangential slices and perform immunohistochemistry. Otherwise, euthanize the pup with an overdose of anesthetic followed by decapitation.
  13. Euthanize the mother mouse with an overdose of anesthetic followed by cervical dislocation.

4. Analysis

  1. Start MATLAB and run EZcalcium toolbox15 to open a graphical user interface (GUI) 'Initial GUI'.
  2. Compensate for the image frame drifts due to mouse movements or other causes.
    1. Click Motion Correction in the Initial GUI to open the Motion Correction GUI. Click 'Add Files...' to load a TIF file of the imaging data.
    2. Set the settings as follows: Non-rigid Motion Correction, blank; Upsampling Factor, 50; Max Shift, 15; Initial Batch Size, 200; Bin Width, 200. Click 'Run Motion Correction' to execute the correction. Motion-corrected imaging data will be saved automatically.
      NOTE: The settings should be adjusted to the imaging data properties. If the drifts of some frames are not compensated because of nonlinear frame distortions or movement of the cortex in the depth direction, open the original imaging data without correction in ImageJ Fiji and remove the frames, and restart step 4.2.
  3. Detect neurons and draw regions of interest (ROIs).
    1. Click Automated ROI Detection in the Initial GUI to open the ROI Detection GUI. Click Add Files... to load the motion-corrected imaging data.
    2. Set the settings as follows: Initialization, Greedy; Search Method, Ellipse; Deconvolution, Constrained FOOPSI-SPGL1; Autoregression, Decay; Estimated # of ROIs, 60 (more than double the number visually detected is recommended); Estimated ROI Width, 17 (~20 µm); Merge Threshold, 0.95; Fudge Factor, 0.95; Spatial Downsampling, 1; Temp. Downsampling, 1; Temp. Iterations, 5.
      NOTE: The settings should be adjusted to the imaging data properties.
    3. Click Run ROI Detection to execute the detection. ROI data will be saved automatically.
    4. Click ROI Refinement in the Initial GUI to open the ROI Refinement GUI. Click Load Data to load the ROI data. Select the ROIs that had low activity frequency (<1 Hz), located under the skull, or contained other neurons' neurites. Click Exclude ROI to exclude the ROIs from the analysis.
    5. Select the Data Export Format to XLSX and click Export Data to obtain an Excel file with raw dF/F values. The dF/F uses equation (1), where F is the average intensity of pixels in every frame, F0 is the baseline signal intensity, and Fb is the background fluorescence.
      Equation 1     (1)
  4. Calculate the Pearson's correlation coefficient of dF/F between ROIs and make a correlation coefficient matrix. Only use dF/F after anesthesia has weakened and spontaneous activity has begun to occur (~10 minutes after stopping isoflurane).
  5. Define the barrel edges from the TCA-RFP image using Fiji. Categorize the ROIs to their respective barrels or septa. Compare the pairwise correlation within the same barrel and that between different barrels.
  6. Generate 1,000 to 10,000 surrogate data by randomly shuffling the correspondence between ROI and Ca2+ traces. Calculate the average correlation coefficient within individual barrels in each surrogate data, and evaluate the statistical significance of the correlation in the real data.
    NOTE: If one of 10,000 surrogates has a value higher than the real value, the statistical significance is 0.0001. The analyses described in steps 4.5 and 4.6 can be conducted for pooled data from multiple animals, as performed elsewhere7,16.

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Representative Results

Figure 1 shows the representative results of layer 4 neuron activities in the barrel cortex of a P6 pup visualized using the present protocol. Two-photon images of the green channel (GCaMP) and red channel (TCA-RFP) were temporally averaged and shown in Figure 1A. Because TCA-RFP fluorescence was much weaker than GCaMP fluorescence, the GCaMP signal leaked into the red channel (Figure 1A1,A2). Fourteen ROIs were drawn on GCaMP-expressing neurons (Figure 1A4). Though the RFP image was clear enough (Figure 1A2), to define barrel edges more precisely, a z-projection image from the 100 µm-thick tangential slice taken by one-photon confocal microscopy was used (Figure 1B,C). The dF/F of 411 second-imaging window, starting ten minutes after stopping isoflurane, is shown in Figure 1D. Movies of GCaMP signals in the same imaging window before and after the movement compensation are also provided (Supplemental Video S1 and Supplemental Video S2).

Figure 2 shows the analysis of activity correlation. The pairwise correlation coefficients within the same barrels (ROI#1-2, ROI#3-7, and ROI#11-12) were higher than those across different barrels (Figure 2A-D). Though the distance from ROI#3 to ROI#4-7 (the same barrel neurons) was longer than that to ROI#12 (a different barrel neuron) (Figure 1C), the correlation was much stronger in the former (Figure 2A,C), indicating that activities synchronized more within individual barrels. The average of correlation coefficients within the same barrels was significantly higher than that calculated from 10,000 sets of surrogate data (Figure 2E). The correlation within the same barrels was significantly strong among three different time windows (Figure 2F,G; compared with surrogate data, all P < 0.001), suggesting that the patchwork-like pattern is independent of anesthetic depth. The septal neuron activity was correlated with both barrel neurons and septal neurons (Figure 2A-C). The specificity of activity correlation from septal neurons to other neurons is yet to be examined.

Figure 1
Figure 1: Calcium activity of barrel area neurons at P6. (A) Two-photon images averaged within the imaging session. (A1) GCaMP signal in the green channel. (A2) RFP signal in the red channel. (A3) Merged image of green and red channels. (A4) Thirteen ROIs drawn on the GCaMP image. (B) One-photon image of the fixed brain tangential slice. (C) The barrel edges defined on the one-photon image. The ROIs in A4 were aligned. The barrel IDs (B1, C2, C3, and D2) are shown.(D) The dF/F of each ROI in a 411-second imaging session starting ten minutes after stopping isoflurane. The location of each ROI (barrel ID or septa) is shown on the left. Scale bars = 100 µm (A1,A2,A3,A4, B,C). Abbreviations: RFP = red fluorescent protein; ROIs = regions of interest; S = septa. Please click here to view a larger version of this figure.

Figure 2
Figure 2: Analysis of calcium activity correlations. (A) The pairwise Pearson's correlation coefficient between all ROIs shown in Figure 1. (B) The P-value of correlation between positively correlated pairs of ROIs. (C) Schematic diagram of correlation strength between the ROIs. The neurons with significant (P < 0.05) positive correlation were connected by lines whose width describes their correlation coefficients. (D) The pairwise correlation coefficient within the same barrels and that across different barrels are plotted. Mean ± S.E.M and P-value of a two-tailed unpaired t-test are shown. (E) The correlation coefficients within the same barrels. Red arrow: actual data; gray bars: histogram of 10,000 surrogate data. (F) The correlations in three separate time windows are shown as in C. Left; first window (1-137 s). Middle; second window (138-274 s). Right; third window (275-411 s).(G) The correlation coefficients are shown as in D for all three windows. Abbreviation: ROIs = regions of interest. Please click here to view a larger version of this figure.

Supplemental Video S1: Patchwork-like activity of L4 neurons in a 411 s imaging session at P6 (10-fold speed) before the movement compensation. Please click here to download this Video.

Supplemental Video S2: Patchwork-like activity of L4 neurons in a 411 s imaging session at P6 (10-fold speed) after the movement compensation. Please click here to download this Video.

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Given that the spontaneous activities emerge from the sensory organ or lower nervous system and travel to the primary sensory area through a pathway equivalent to that of a mature nervous system3, it is crucial to define the primary sensory area and the location of imaged neurons within the area. In this protocol, we addressed this requirement by employing transgenic mice that visualize thalamocortical axons and the Supernova system that expresses GCaMP sparsely8. These techniques enabled the analysis of activity patterns within each sensory area as well as within the intra-areal subfields, offering a means of investigating the developmental mechanisms of sensory systems.

While this protocol summarizes how to observe patchwork-like activity within the S1 barrel area, it is also applicable to observe unique activity patterns in other cortical areas, as demonstrated in V17. Some activities synchronize or propagate across multiple cortices, which have mainly been studied using single-photon imaging3,17,18,19. The recently established wide-field two-photon imaging techniques20,21, combined with gene-introducing techniques using virus vectors and transgenic mice22,23, will enable the simultaneous assessment of area-specific and inter-areal activities at a single-cell resolution.

For the analysis of interneuronal correlations, signal contamination between neurons can lead to erroneous outcomes. One solution is to express GCaMP sparsely, as we performed with the Supernova system8. Another solution is to reduce signal contamination using computational methods24 or cell body-targeted GCaMP expression25. Additionally, while ROIs can be determined manually with Fiji or other software7,14, computer programs with appropriate algorithms provide more rigorous and reproducible ROI settings. Automated segmentation tools like CaImAn26, Suite2p27, and EZcalcium15 can enable such settings. Experimenters should consider employing a suitable tool based on the data type they deal with, available software, and programming skills.

TCA-RFP mice enabled us to delineate primary sensory areas and layer 4 during imaging7, ensuring precise imaging. However, transgenic mice's introduction and timed mating can be time-consuming and demanding. Alternatively, primary sensory areas can be visualized after imaging by VGluT2 immunostaining that labels thalamocortical axon terminals. A two-dimensional arrangement of these areas can be visualized with tangential slices and imaged by one-photon confocal microscopy7.

A limitation of this protocol is that isoflurane anesthesia affects spontaneous neuronal activity in neonates4,7,28. In the representative results, activities within the same barrels remained consistently synchronized as the anesthesia lessened, suggesting that the patchwork-like pattern is resilient to variations in anesthetic depth. Nevertheless, a new technique is required to remove restraint stress from neonatal pups and enable fully awake state imaging.

The synchronous activity patterns are primarily shaped by peripheral activity via thalamocortical inputs3,4,17, which may be altered as intracortical connections mature and come to predominate within the cortical network29,30,31. Intracortical connection types may also contribute to the pattern changes. The connections between cortical excitatory neurons are largely governed by gap junctions that facilitate synchronous activity during the first postnatal week16,32,33,34,35, which are replaced by recurrent synaptic connections in the second postnatal week32,35. These transitions may change activity correlations, which can be evaluated by neuronal assembly detection techniques36 (also see37). Ideally, chronic imaging spanning two weeks may fully assess such changes in the same animal. However, chronic neonatal imaging is currently limited to up to four days38, due to the resin encasing that affects brain development and the inflammatory response that lowers pial surface transparency. A novel technique to image neuronal activities in broader space and time will lead to a better understanding of brain circuit formation.

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The authors have no competing financial interests to declare.


This work was supported by the Japan Society for the Promotion of Science Grants-in-Aid for Transformative Research Areas (B) (22H05092, 22H05094) and for Scientific Research Grants 20K06876, AMED under Grant Number 21wm0525015, the Takeda Science Foundation, the Naito Foundation, the Kato Memorial Bioscience Foundation, the Kowa Life Science Foundation, NIG-JOINT (24A2021) (to H.M.); and Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grants 19K06887 and 22K06446, the Kodama Memorial Fund for Medical Research, the Uehara Memorial Foundation, the Kato Memorial Bioscience Foundation, and the Takeda Science Foundation (to N.N-T.). We thank Dr. Takuji Iwasato for the TCA-RFP mice.


Name Company Catalog Number Comments
20× objective lens (water immersion)
250 mL Vacuum Filter/Storage Bottle System Corning 431096
4%-paraformaldehyde phosphate buffer solution (4% PFA) Nacalai 09154-85
Acrylic resin (UNIFAST II) GC N/A
Agarose Sigma A9793
Aspirator tube assembly Drummond 2-040-000
CaCl2•2H2O Nacalai 06731-05
Electroporator BEX GEB14
Eye drop (Scopisol) Senju Pharmaceutical N/A
Fluorescence stereo microscope Leica M165FC
Glucose Nacalai 16806-25
Heating pad Muromachi Kikai FHC-HPS
HEPES Gibco 15630-080
Isoflurane Pfizer N/A
KCl Nacalai 28514-75
MgSO4•7H2O Wako 131-00405
Micropipette puller Narishige PC-100
Multiphoton laser Spectra-Physics Mai Tai eHP DeepSee
Multiphoton microscope Zeiss LSM 7MP
NaCl Nacalai 31320-05
Non-woven fabric (Kimwipe) Kimberly Clark S-200
Phosphate buffered saline (PBS) Nacalai 27575-31
Plasmid: CAG-loxP-STOP-loxP-GCaMP6s-ires-tTA-WPRE Addgene pK175
Plasmid: TRE-nCre Addgene pK031
Precision calibrated micropipets Drummond 2-000-050
Razor blade Feather FA-10
Rimadyl (50 mg/mL Carprofen) Zoetis JP N/A
Round cover glass, 3-mm-diameter  Matsunami CS01078
Saline Otsuka 035175315
Sodium pentobarbital Nacalai 26427-72
Stage for imaging living pup (two single-axis translation stage for XY positioning, two-axis goniometer, base plate, adjustable pillar for z positioning) ThorLabs LT1/M, GN2/M, BM2060/M, MLP01/M
TCA-RFP mouse N/A N/A Mizuno et al., 2018a
Tissue adhesive (Vetbond) 3M 1469SB
Titanium bar Endo Scientific Instrument N/A Custom made (Mizuno et al., 2018b)
Titanium bar fixing plate N/A Custom made (Mizuno et al., 2018b)
Trypan blue Sigma T8154
Tweezers with platinum plate electrode, 5 mm diameter BEX CUY650P5
Wild-type ICR mouse Nihon SLC Slc:ICR



  1. Rao, M. S., Mizuno, H. Elucidating mechanisms of neuronal circuit formation in layer 4 of the somatosensory cortex via intravital imaging. Neuroscience Research. 167, 47-53 (2021).
  2. Iwasato, T., Erzurumlu, R. S. Development of tactile sensory circuits in the CNS. Current Opinion in Neurobiology. 53, 66-75 (2018).
  3. Martini, F. J., Guillamón-Vivancos, T., Moreno-Juan, V., Valdeolmillos, M., López-Bendito, G. Spontaneous activity in developing thalamic and cortical sensory networks. Neuron. 109 (16), 2519-2534 (2021).
  4. Ackman, J. B., Burbridge, T. J., Crair, M. C. Retinal waves coordinate patterned activity throughout the developing visual system. Nature. 490 (7419), 219-225 (2012).
  5. Tritsch, N. X., Yi, E., Gale, J. E., Glowatzki, E., Bergles, D. E. The origin of spontaneous activity in the developing auditory system. Nature. 450 (7166), 50-55 (2007).
  6. Babola, T. A., et al. Homeostatic control of spontaneous activity in the developing auditory system. Neuron. 99 (3), 511-524.e5 (2018).
  7. Mizuno, H., et al. Patchwork-type spontaneous activity in neonatal barrel cortex layer 4 transmitted via thalamocortical projections. Cell Reports. 22 (1), 123-135 (2018).
  8. Mizuno, H., et al. NMDAR-regulated dynamics of layer 4 neuronal dendrites during thalamocortical reorganization in neonates. Neuron. 82 (2), 365-379 (2014).
  9. Tabata, H., Nakajima, K. Efficient in utero gene transfer system to the developing mouse brain using electroporation: visualization of neuronal migration in the developing cortex. Neuroscience. 103 (4), 865-872 (2001).
  10. Fukuchi-Shimogori, T., Grove, E. A. Neocortex patterning by the secreted signaling molecule FGF8. Science. 294 (5544), 1071-1074 (2001).
  11. Saito, T., Nakatsuji, N. Efficient gene transfer into the embryonic mouse brain using in vivo electroporation. Developmental Biology. 240 (1), 237-246 (2001).
  12. Holtmaat, A., et al. Long-term, high-resolution imaging in the mouse neocortex through a chronic cranial window. Nature Protocols. 4 (8), 1128-1144 (2009).
  13. Mizuno, H., Nakazawa, S., Iwasato, T. In vivo two-photon imaging of cortical neurons in neonatal mice. Journal of Visualized Experiments. 140, e58340 (2018).
  14. Egashira, T., et al. In vivo two-photon calcium imaging of cortical neurons in neonatal mice. STAR Protocols. 4 (2), 102245 (2023).
  15. Cantu, D. A., et al. EZcalcium: Open-source toolbox for analysis of calcium imaging data. Frontiers in Neural Circuits. 14, 25 (2020).
  16. Maruoka, H., et al. Lattice system of functionally distinct cell types in the neocortex. Science. 358 (6363), 610-615 (2017).
  17. Antón-Bolaños, N., et al. Prenatal activity from thalamic neurons governs the emergence of functional cortical maps in mice. Science. 364 (6444), 987-990 (2019).
  18. Guillamón-Vivancos, T., et al. Input-dependent segregation of visual and somatosensory circuits in the mouse superior colliculus. Science. 377 (6608), 845-850 (2022).
  19. Cardin, J. A., Crair, M. C., Higley, M. J. Mesoscopic imaging: Shining a wide light on large-scale neural dynamics. Neuron. 108 (1), 33-43 (2020).
  20. Chen, J. L., Voigt, F. F., Javadzadeh, M., Krueppel, R., Helmchen, F. Long-range population dynamics of anatomically defined neocortical networks. eLife. 5, e14679 (2016).
  21. Ota, K., et al. cell-resolution, contiguous-wide two-photon imaging to reveal functional network architectures across multi-modal cortical areas. Neuron. 109 (11), 1810-1824 (2021).
  22. Zariwala, H. A., et al. A Cre-dependent GCaMP3 reporter mouse for neuronal imaging in vivo. The Journal of Neuroscience. 32 (9), 3131-3141 (2012).
  23. Murakami, T., Matsui, T., Uemura, M., Ohki, K. Modular strategy for development of the hierarchical visual network in mice. Nature. 608 (7923), 578-585 (2022).
  24. Pnevmatikakis, E. A., et al. Simultaneous denoising, deconvolution, and demixing of Calcium imaging data. Neuron. 89 (2), 285-299 (2016).
  25. Shemesh, O. A., et al. Precision calcium imaging of dense neural populations via a cell-body-targeted calcium indicator. Neuron. 107 (3), 470-486 (2020).
  26. Giovannucci, A., et al. CaImAn an open source tool for scalable calcium imaging data analysis. Elife. 8, e38173 (2019).
  27. Pachitariu, M., et al. Suite2p: beyond 10,000 neurons with standard two-photon microscopy. BioRxiv. , (2017).
  28. Sitdikova, G., et al. Isoflurane suppresses early cortical activity. Annals of Clinical and Translational Neurology. 1 (1), 15-26 (2014).
  29. Marques-Smith, A., et al. A Transient translaminar GABAergic interneuron circuit connects thalamocortical recipient layers in neonatal somatosensory cortex. Neuron. 89 (3), 536-549 (2016).
  30. Tuncdemir, S. N., et al. Early somatostatin interneuron connectivity mediates the maturation of deep layer cortical circuits. Neuron. 89 (3), 521-535 (2016).
  31. Nakazawa, S., Yoshimura, Y., Takagi, M., Mizuno, H., Iwasato, T. Developmental phase transitions in spatial organization of spontaneous activity in postnatal barrel cortex layer 4. The Journal of Neuroscience. 40 (40), 7637-7650 (2020).
  32. Yu, Y. -C., et al. Preferential electrical coupling regulates neocortical lineage-dependent microcircuit assembly. Nature. 486 (7401), 113-117 (2012).
  33. Siegel, F., Heimel, J. A., Peters, J., Lohmann, C. Peripheral and central inputs shape network dynamics in the developing visual cortex in vivo. Current Biology. 22 (3), 253-258 (2012).
  34. Nakagawa, N., Hosoya, T. Slow dynamics in microcolumnar gap junction network of developing neocortical pyramidal neurons. Neuroscience. 406, 554-554 (2019).
  35. Valiullina, F., et al. Developmental changes in electrophysiological properties and a transition from electrical to chemical coupling between excitatory layer 4 neurons in the rat barrel cortex. Frontiers in Neural Circuits. 10, 1 (2016).
  36. Avitan, L., et al. Spontaneous and evoked activity patterns diverge over development. Elife. 10, e61942 (2021).
  37. Mölter, J., Avitan, L., Goodhill, G. J. Detecting neural assemblies in calcium imaging data. BMC Biology. 16 (1), 143 (2018).
  38. Nakazawa, S., Mizuno, H., Iwasato, T. Differential dynamics of cortical neuron dendritic trees revealed by long-term in vivo imaging in neonates. Nature Communications. 9 (1), 3106 (2018).
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Nakagawa-Tamagawa, N., Egashira, T., More

Nakagawa-Tamagawa, N., Egashira, T., Rao, M. S., Mizuno, H. In Vivo Visualization of Spontaneous Activity in Neonatal Mouse Sensory Cortex at a Single-Neuron Resolution. J. Vis. Exp. (201), e65899, doi:10.3791/65899 (2023).

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