This work was supported by a Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant #40352, Campus Alberta for Innovation Program Chair, Alberta Alzheimer Research Program to MHM, and NSERC CREATE in BIF doctoral fellowship and AIHS postgraduate fellowship to MK. We thank Pu Min Wang for the development of this protocol and for surgical training, and Behroo Mirza Agha and Di Shao for husbandry.

The following protocol follows the University of Lethbridge Animal Care Committee (ACC) guidelines, and is conducted in accordance with the standards of the Canadian Council on Animal Care (CCAC).
1. Preparation
<ol>
	<li>For prolonged study periods, autoclave all opened surgical supplies and ensure that sterility is maintained throughout the surgery. If multiple surgeries are required, autoclave between surgeries.&#160;</li>
	<li>Ensure there is plenty of brain buffer on hand (at least 50 m...

<ol>
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H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Voltage-sensitive+dye+imaging+reveals+dynamic+spatiotemporal+properties+of+cortical+activity+after+spontaneous+muscle+twitches+in+the+newborn+rat.">Voltage-sensitive dye imaging reveals dynamic spatiotemporal properties of cortical activity after spontaneous muscle twitches in the newborn rat.</a> J Neurosci. 32 (32), 10982-10994 (2012).</li><li>Sweetnam, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Diabetes+impairs+cortical+plasticity+and+functional+recovery+following+ischemic+stroke.">Diabetes impairs cortical plasticity and functional recovery following ischemic stroke.</a> J Neurosci. 32 (15), 5132-5143 (2012).</li><li>Yin, Y. Q., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vivo+field+recordings+effectively+monitor+the+mouse+cortex+and+hippocampus+under+isoflurane+anesthesia.">In vivo field recordings effectively monitor the mouse cortex and hippocampus under isoflurane anesthesia.</a> Neural Regeneration Research. 11 (12), 1951-1955 (2016).</li><li>Sharp, P. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+stimulus-evoked+cerebral+hemodynamics+in+the+awake+mouse+and+under+a+novel+anesthetic+regime.">Comparison of stimulus-evoked cerebral hemodynamics in the awake mouse and under a novel anesthetic regime.</a> Scientific Reports. 5, 12621 (2015).</li><li>Kyweriga, M., Mohajerani, M. H., Kianianmomeni, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optogenetics:+Methods+and+Protocols.">Optogenetics: Methods and Protocols.</a> Methods in Molecular Biology. 1408, 251-265 (2016).</li><li>Grutzendler, J., Gan, W. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Imaging in neuroscience and development : a laboratory manual. , (2005).</li><li>Vanni, M. P., Murphy, T. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mesoscale+transcranial+spontaneous+activity+mapping+in+GCaMP3+transgenic+mice+reveals+extensive+reciprocal+connections+between+areas+of+somatomotor+cortex.">Mesoscale transcranial spontaneous activity mapping in GCaMP3 transgenic mice reveals extensive reciprocal connections between areas of somatomotor cortex.</a> J Neurosci. 34 (48), 15931-15946 (2014).</li><li>Xie, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Resolution+of+High-Frequency+Mesoscale+Intracortical+Maps+Using+the+Genetically+Encoded+Glutamate+Sensor+iGluSnFR.">Resolution of High-Frequency Mesoscale Intracortical Maps Using the Genetically Encoded Glutamate Sensor iGluSnFR.</a> J Neurosci. 36 (4), 1261-1272 (2016).</li><li>Chan, A. W., Mohajerani, M. H., LeDue, J. M., Wang, Y. T., Murphy, T. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mesoscale+infraslow+spontaneous+membrane+potential+fluctuations+recapitulate+high-frequency+activity+cortical+motifs.">Mesoscale infraslow spontaneous membrane potential fluctuations recapitulate high-frequency activity cortical motifs.</a> Nat Commun. 6, 7738 (2015).</li><li>Lim, D. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vivo+Large-Scale+Cortical+Mapping+Using+Channelrhodopsin-2+Stimulation+in+Transgenic+Mice+Reveals+Asymmetric+and+Reciprocal+Relationships+between+Cortical+Areas.">In vivo Large-Scale Cortical Mapping Using Channelrhodopsin-2 Stimulation in Transgenic Mice Reveals Asymmetric and Reciprocal Relationships between Cortical Areas.</a> Front Neural Circuits. 6, (2012).</li><li>Ferezou, I., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spatiotemporal+dynamics+of+cortical+sensorimotor+integration+in+behaving+mice.">Spatiotemporal dynamics of cortical sensorimotor integration in behaving mice.</a> Neuron. 56 (5), 907-923 (2007).</li><li>Mohajerani, M. H., Aminoltejari, K., Murphy, T. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Targeted+mini-strokes+produce+changes+in+interhemispheric+sensory+signal+processing+that+are+indicative+of+disinhibition+within+minutes.">Targeted mini-strokes produce changes in interhemispheric sensory signal processing that are indicative of disinhibition within minutes.</a> Proc Natl Acad Sci U S A. 108 (22), E183-E191 (2011).</li><li>Madisen, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transgenic+mice+for+intersectional+targeting+of+neural+sensors+and+effectors+with+high+specificity+and+performance.">Transgenic mice for intersectional targeting of neural sensors and effectors with high specificity and performance.</a> Neuron. 85 (5), 942-958 (2015).</li></ol>

This innovative protocol for a large cranial window enables simultaneous imaging over the temporal and parietal areas of the cerebral cortex. Combined with optical imaging, it can help to reveal neural dynamics within cortical areas during spontaneous and stimulus-induced activity. This expansive craniotomy also exposes a large extension of the cortical vasculature network, including the proximal end of the middle cerebral artery (MCA), enabling in vivo imaging of blood flow and direct manipulation of lateral ve...

The craniotomy is a standard procedure used by neuroscientists to reveal a portion of the brain. Since the dawn of electrophysiology, the craniotomy has allowed unprecedented breakthroughs in the field of neuroscience. Dense mapping of the cerebral cortex with electrodes has led to experiments testing hypotheses and theories based on these maps. We have recently entered a new era where the craniotomy is being utilized for in vivo imaging of cortical blood flow1,2,3 and neurovascular architecture4, enabling real time visualization of cortical activity within the exposed areas5,6,7. Although many studies use craniotomies combined with in vivo optical imaging techniques to study the structure and function of cortical neurons, glia, and cortical vasculature8,9, further investigations are limited by small areas of exposed cortex (but see10).
The purpose of this protocol is to provide a method for creating a large lateral craniotomy, exposing the cerebral cortex from the midline to the squamosal bone, and extending beyond bregma and lambda. This large craniotomy enables simultaneous viewing of the association cortices (retrosplenial, cingulate, and parietal), primary and secondary motor, somatosensory, visual, and the auditory cortex. This method has been previously coupled with voltage sensitive dye imaging (VSDI) to investigate how multiple cortical areas interact with one another during spontaneous and stimulus-induced cortical activity5,11,12. The most challenging aspects of this procedure include positioning the head of the animal, fixing the head plate, and avoiding hemorrhage while separating the temporal muscle from the parietal bone. Care must also be taken during the drilling and skull removal processes as the skull curves at an oblique angle.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Heating Pad&#160;</td>
			<td>FHC</td>
			<td>40-90-2</td>
			<td></td>
		</tr>
		<tr>
			<td>Fine Scissors</td>
			<td>Fine Science Tools</td>
			<td>14058-09</td>
			<td></td>
		</tr>
		<tr>
			<td>Forceps&#160;</td>
			<td>Fine Science Tools</td>
			<td>11251-35</td>
			<td>2 or more pairs are recommended</td>
		</tr>
		<tr>
			<td>Spring scissors</td>
			<td>Fine Science Tools</td>
			<td>15000-00, 15000-10</td>
			<td>1 pair should be designated for dura removal&#160;</td>
		</tr>
		<tr>
			<td>Jet tooth shade powder</td>
			<td>LANG Dental</td>
			<td>Jet Tooth Shade Powder</td>
			<td>to be mixed with the Jet Liquid</td>
		</tr>
		<tr>
			<td>Jet tooth shade liquid</td>
			<td>LANG Dental</td>
			<td>Jet Tooth Shade Liquid</td>
			<td>to be mixed wihth the Jet Powder&#160;</td>
		</tr>
		<tr>
			<td>Drill Heads - Carbide Burs FG 1/4 389</td>
			<td>Midwest Dental</td>
			<td>385201</td>
			<td></td>
		</tr>
		<tr>
			<td>Agarose Powder</td>
			<td>Sigma-Aldrich</td>
			<td>A9793</td>
			<td></td>
		</tr>
		<tr>
			<td>Gelfoam</td>
			<td>Sinclair Dental Canada</td>
			<td>Pfizer Gelfoam</td>
			<td></td>
		</tr>
		<tr>
			<td>Isoflurane</td>
			<td>Western Drug Distribution Centre Ltd</td>
			<td>124125</td>
			<td></td>
		</tr>
		<tr>
			<td>Lidocaine 2% Epinephrine</td>
			<td>Western Drug Distribution Centre Ltd</td>
			<td>125299</td>
			<td></td>
		</tr>
		<tr>
			<td>Dexamethazone 5 mg/mL</td>
			<td>Western Drug Distribution Centre Ltd</td>
			<td>125231</td>
			<td></td>
		</tr>
		<tr>
			<td>Butyl cyanoacrylate glue (VetBond)</td>
			<td>Western Drug Distribution Centre Ltd</td>
			<td>12612</td>
			<td></td>
		</tr>
	</tbody>
</table>

a large lateral craniotomy procedure for mesoscale wide-field optical imaging of brain activity

The craniotomy is a commonly performed procedure to expose the brain for in vivo experiments. In mouse research, most labs utilize a small craniotomy, typically 3 mm x 3 mm. This protocol introduces a method for creating a substantially larger 7 mm x 6 mm cranial window exposing most of a cerebral hemisphere over the mouse temporal and parietal cortices (e.g., bregma 2.5 - 4.5 mm, lateral 0 - 6 mm). To perform this surgery, the head must be tilted approximately 30&#176; and much of the temporal muscle must be retracted. Due to the large amount of bone removal, this procedure is intended only for acute experiments with the animal anesthetized throughout the surgery and experiment.
The main advantage of this innovative large lateral cranial window is to provide simultaneous access to both medial and lateral areas of the cortex. This large unilateral cranial window can be used to study the neural dynamics between cells, as well as between different cortical areas by combining multi-electrode electrophysiological recordings, imaging of neuronal activity (e.g., intrinsic or extrinsic imaging), and optogenetic stimulation. Additionally, this large craniotomy also exposes a large area of cortical blood vessels, allowing for direct manipulation of the lateral cortical vasculature.

To study the interactions between cortical areas within a single hemisphere, we used a large craniotomy extending across the sagittal sinus and 5 - 6 mm lateral. This cranial window included primary (motor, somatosensory, visual, auditory), secondary (motor, visual), and association (retrosplenial, cingulate, parietal association) cortices of right brain hemispheres (Figure 3A). For this work we used voltage sensitive dye (VSD) imaging, which reflects changes...

Watch this Scientific Journal Video about A Large Lateral Craniotomy Procedure for Mesoscale Wide-field Optical Imaging of Brain Activity at JoVE.com

A Large Lateral Craniotomy Procedure for Mesoscale Wide-field Optical Imaging of Brain Activity

This protocol presents a method for creating a large unilateral craniotomy over the temporal and parietal regions of the mouse cerebral cortex. This is especially useful for real time imaging over an expansive area of a cortical hemisphere.

The craniotomy is a commonly performed procedure to expose the brain for in vivo experiments. In mouse research, most labs utilize a small craniotomy, ...

The overall goal of this large lateral craniotomy is to perform real time imaging over an expansive area of a cortical hemisphere. The main advantage of this technique is that large areas of the cortex are exposed for observation and can be used in conjunction with technologies such as optogenetics. This technique can provide insights into characterizing the neural dynamics between cells as well as that between different brain circuits at different temporal and spatial resolutions.Visual demonstration of this method is critical due to the increased risk of hemmorage and cortical damage since the dura is often attached to brain surface and blood vessels. This method can be applied to study the neurobiological mechanisms underlying brain circuit development and its changes throughout life in response to new experiences or pathologies such as Alzheimer's Disease or stroke. To begin this procedure, autoclave all the surgical supplies and ensure that sterility is maintained throughout the surgery.Ensure there is enough brain buffer for the surgery. Next, transfer an anesthetized mouse to the head holder setup and place it on a thermo-regulating heating pad set to 37 degrees Celsius. Secure the mouse's upper teeth in a teeth holder.Then rotate its head towards the left approximately 30 degrees to expose the right lateral side of the head. Subsequently, secure the mouse's head with the blunt end of the ear bars. Then apply a thalmic ointment to prevent corneal drying.To reduce cerebral edema, inject it with dexamethasone at four milligrams per kilogram intermuscularly. Wipe the skin over the surgical area with cotton swabs dipped in 4%chlorhexidine three times and then with 70%alcohol three times. Inject lidocaine subcutaneously over the craniotomy site.Under a dissecting microscope, lift up the skin at one millimeter left of the midline just behind the ear with forceps and make a small horizontal incision with surgical scissors. Make a five to six millimeter lateral cut towards the right ear and then cut towards the rostral end of the head. At the initial incision point, insert the scissors and cut 10 millimeters rostrally.After that, cut the skin around the right ear and near the right eye to expose the right side of the skull and temporal muscle. Ensure that the widest part of the exposed area is at least seven millimeters. Then trim the skin further if the surgical area needs to be extended.Using a cotton swab, rub the surface of the skull in a circular motion to remove the periosteum from the skull. Ensure that no periosteum remains and that the skull is completely dry, which is critical for successful attachment of the head plate. Next, using spring scissors and forceps, separate the temporal muscle from the skull.Cut and retract the muscle laterally until it reaches the squamosal bone. Take extreme care not to damage the superficial temporal vein that runs along the level of the squamosal bone near the eye, otherwise hemorrhage might occur. Control bleeding with gel foam pre-soaked in brain buffer.For serious hemorrhage, use a heat cauterizer. Drop butyl cyanoacrylate glue onto bleeding sites. To begin this procedure, first mark bregma to orient the underlying brain regions, apply ethyl cyanoacrylate glue around the bottom edge of the head plate and glue the head plate over the craniotomy area.After that, fill the opening space between the skull and the head plate with dental cement, leaving only the craniotomy area exposed. Then wait for the dental cement to dry and harden. Subsequently, outline the cranial window region by lightly scoring the surface of the skull with the dental drill.Gently trace the drill along the original scoring to deepen it, ensuring that the drill does not penetrate through the skull into the brain. In the meantime, switch between drilling and dabbing the skull's surface with moistened rolled tissues every few minutes. This very challenging start requires surgeons to drill through the aged skull to free it for removal without damaging the underlying cortex.Slow is loose, smooth is fast. During drilling, periodically check for buckling of the skull by gently pressing on it with forceps or the non-moving drill bit. When the bone begins the buckle, stop drilling and immerse the entire window in brain buffer.Wait for at least five minutes before skull removal to soften the bone and to reduce the chance of the dura sticking to the bone, making the skull removal process easier. Next, perform the skull removal process beginning at the anterior edge. Gently pry the loose skull from the dura using forceps.Once the bone is loose and floating on the dura, firmly grasp it with forceps and lift it away from the dura. Ensure the bone never penetrates into the brain. Use forceps and spring scissors to gently tear and cut away the dura.Care must be taken to ensure the brain parenchyma and blood vessels are not damaged. Continue until all dura is removed from the cranial window site. When performed correctly, the brain will appear to be very clean with distinct blood vessels and no blemishes.Spray the coverglass with 70%ethanol and use an air canister to gently dry. Ensure the glass is completely clean with no spots or dust present. Next, prepare 1.3%agarose by heating 200 milligrams of agarose powder dissolved in 15 milliliters of brain buffer.Place a thermometer in the hot agarose and cool the agarose down to just above solidifying temperature at about 40 degrees Celsius. Cooling can be expedited by running cold water over the tube, taking care not to allow any water to enter the agar. Gently stir with the thermometer while monitoring its temperature.Immediately before applying the agar, remove the brain buffer from the cranial well. Ensure no bubbles or particles are present as these will interfere with imaging. Now draw up the agarose with a transfer pipe head and drop the agarose directly on the brain.Then quickly place the coverslip over the surface and fasten the coverslip with the agarose drops on the corners. Shown here is a photo micrograph of the wide unilateral craniotomy with bregma indicated by a white circle in each image. Patterns of cortical activation are shown in a mouse anesthetized with 0.5%isoflurane after stimulation of the contralateral whisker, auditory stimulation, contralateral forelimb stimulation, contralateral hindlimb stimulation and visual stimulation of the contralateral eye with a light-emitting diode.There was midline activation from all forms of sensory stimulation at 10 to 25 milliseconds after primary sensory cortex activation. Once mastered, this technique can be completed in three to four hours. When attempting this procedure, it's important to remember to keep the blood loss to minimum and to ensure the cortex is not damaged.Using this procedure, other imaging techniques such as optical imaging can help to answer important questions such as how neural dynamics are influenced by spontaneous activity in the normal and diseased brain. Following its development, this technique helped to pave the way for researchers in the field of systems neuroscience to explore interactions and neural dynamics between widely spaced cortical regions in mice. This video shows you how to perform a large lateral craniotomy in the mouse with minimal blood loss and cortical damage, enabling you to collect the necessary data to answer your most pressing scientific questions.

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12.1K vistas.  University of Lethbridge. The overall goal of this large lateral craniotomy is to perform real time imaging over an expansive area of a cortical hemisphere. The main advantage of this technique is that large areas of the cortex are exposed for observation and can be used in conjunction with technologies such as optogenetics. This technique can provide insights into characterizing the neural dynamics between cells as well as that between different brain circuits at different temporal and spatial resolutions.Visu...

Video: A Large Lateral Craniotomy Procedure for Mesoscale Wide-field Optical Imaging of Brain Activity

This protocol presents a method for creating a large unilateral craniotomy over the temporal and parietal regions of the mouse cerebral cortex. This is especially useful for real time imaging over an expansive area of a cortical...

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Deep-Tissue Three-Photon Fluorescence Microscopy in Intact Mouse and Zebrafish Brain

Three-photon microscopy enables high-contrast fluorescence imaging deep in living biological tissues, such as mouse and zebrafish brains, with high spatiotemporal...

assessment of thermal damage from robot-drilled craniotomy for cranial window surgery in mice

Assessment of Thermal Damage from Robot-Drilled Craniotomy for Cranial Window Surgery in Mice

Cranial windows have become a ubiquitously implemented surgical technique to allow for intravital imaging in transgenic mice. This protocol describes the use of a surgical robot that performs semi-automated bone drilling of cranial windows and can help reduce surgeon-to-surgeon variability and partially mitigate thermal blood-brain barrier...

a craniotomy surgery procedure for chronic brain imaging

A Craniotomy Surgery Procedure for Chronic Brain Imaging

This video and protocol demonstrate how to implant a glass-covered cranial window in rodents. These preparations can be used for chronic in vivo two-photon imaging of the neocortex over time scales of months. It may also be used for other types of imaging, including optical intrinsic signal...

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In Vivo Wide-Field and Two-Photon Calcium Imaging from a Mouse Using a Large Cranial Window

The present protocol describes making a large (6 x 3 mm2) cranial window using food wrap, transparent silicone, and cover glass. This cranial window allows in vivo wide-field and two-photon calcium imaging experiments in the same...

In Vivo Wide-Field and Two-Photon Calcium Imaging from a Mouse Using a Large Cranial Window

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Wide-field Single-photon Optical Recording in Brain Slices Using Voltage-sensitive Dye

We introduce a reproducible and stable optical recording method for brain slices using voltage-sensitive dye. The article describes voltage-sensitive dye staining and recording of optical signals using conventional hippocampal slice...

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Automated Behavioral Analysis of Large C. elegans Populations Using a Wide Field-of-view Tracking Platform

We describe protocols for using the wide field-of-view nematode tracking platform (WF-NTP), which enables high-throughput phenotypic characterization of large populations of Caenorhabditis elegans. These protocols can be used to characterize subtle behavioral changes in mutant strains or in response to pharmacological treatment in a highly scalable fashion.

Automated Behavioral Analysis of Large C. elegans Populations Using a Wide Field-of-view Tracking Platform

optical clearing and labeling for light-sheet fluorescence microscopy in large-scale human brain imaging

Author Spotlight: Advancing 3D Cytoarchitecture Analysis - Rapid Volumetric Reconstruction of the Human Brain 

The present protocol provides a step-by-step procedure for rapid and simultaneous optical clearing, muti-round labeling, and 3D volumetric reconstruction of tens of postmortem human brain sections by combining the (SWITCH - H2O2 - Antigen Retrieval - 2,2'-thiodiethanol [TDE]) SHORT tissue transformation technique with light-sheet fluorescence microscopy imaging in a routinely high-throughput...

Optical Clearing and Labeling for Light-sheet Fluorescence Microscopy in Large-scale Human Brain Imaging

craniotomy procedure for visualizing neuronal activities in hippocampus of behaving mice

Craniotomy Procedure for Visualizing Neuronal Activities in Hippocampus of Behaving Mice

This article demonstrates the preparation of a custom-made imaging window supplemented with infusion cannula and its implantation onto the CA1 region of the hippocampus in mice.

wide-field fluorescent microscopy and fluorescent imaging flow cytometry on a cell-phone

Wide-field Fluorescent Microscopy and Fluorescent Imaging Flow Cytometry on a Cell-phone

We review our recent results on the integration of fluorescent microscopy and imaging flow cytometry tools on a cell-phone using compact and cost-effective opto-fluidic attachments. These cell-phone based micro-analysis devices might be useful for cytometric analysis, such as performing various cell counting tasks as well as for high-throughput screening of e.g., water samples in resource limited...

wide-field calcium imaging of mouse superior colliculus neurons

Wide-Field Calcium Imaging of Mouse Superior Colliculus Neurons  

long-term imaging mammalian cells using wide-field microscopy

Long-term Imaging Mammalian Cells using Wide-Field Microscopy

optical recording of neuronal activity in brain slices stained with a voltage-sensitive dye

This video demonstrates a procedure for observing changes in neuronal activity in a brain slice stained with a voltage-sensitive dye. The dye reflects changes in the neuron&#39;s membrane potential by altering its fluorescence intensity. Through the application of electrical stimuli and advanced imaging techniques, this process enables visual tracking of real-time changes in neuronal membrane potential based on VSD...

Optical Recording of Neuronal Activity in Brain Slices Stained with a Voltage-Sensitive Dye

implantation of cranial imaging window in mouse model: a surgical procedure to implant glass-based coverslip for stable optical access to regions of murine brain

This video presents a surgical procedure to implant cranial window in a mouse model for stable optical access to different regions of the...

Implantation of Cranial Imaging Window in Mouse Model: A Surgical Procedure to Implant Glass-based Coverslip for Stable Optical Access to Regions of Murine Brain

a semiautomated chip-seq procedure for large-scale epigenetic studies

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

This paper describes a semiautomated, microscaled ChIP-Seq protocol of DNA regions associated with a specific histone modification (H3K27ac) using a ChIP liquid-handler platform, followed by library preparation using tagmentation. The procedure includes control assessment for quality and quantity purposes and can be adopted to other histone modifications or transcription...

single plane illumination module and micro-capillary approach for a wide-field microscope

Single Plane Illumination Module and Micro-capillary Approach for a Wide-field Microscope

A module for single plane illumination microscopy (SPIM) is described which is easily adapted to an inverted wide-field microscope and optimized for 3-dimensional cell cultures. The sample is located within a rectangular capillary, and via a microfluidic system fluorescent dyes, pharmaceutical agents or drugs can be applied in small...

wide-field, real-time imaging of local and systemic wound signals in arabidopsis

Wide-Field, Real-Time Imaging of Local and Systemic Wound Signals in Arabidopsis

Extracellular glutamate-triggered systemic calcium signaling is critical for the induction of plant defense responses to mechanical wounding and herbivore attack in plants. This article describes a method to visualize the spatial and temporal dynamics of both these factors using Arabidopsis thaliana plants expressing calcium- and glutamate-sensitive fluorescent...

Wide-Field, Real-Time Imaging of Local and Systemic Wound Signals in Arabidopsis

live imaging of the ependymal cilia in the lateral ventricles of the mouse brain

Live Imaging of the Ependymal Cilia in the Lateral Ventricles of the Mouse Brain

Using high-resolution differential interference contrast (DIC) microscopy, an ex vivo observation of the beating of motile ependymal cilia located within the mouse brain ventricles is demonstrated by live-imaging. The technique allows a recording of the unique ciliary beating frequency and beating angle as well as their intracellular calcium oscillation pacing...

Then, adjust the height of the suction pipette so that the liquid level inside the experiment chamber is always constant. Place the ground electrode in the chamber. Subsequently, fill the glass electrode with a small amount of aCSF, and place it in the electrode holder. Attach the holder to the rod of the...

Use a heating lamp to preserve the body temperature and apply ointment to the animal&#39;s eyes. Using sharp scissors, shave the fur on the skull from the eyes to the base of the skull, and use 70% ethanol to sterilize the exposed...

State-Dependency Effects on TMS:  A Look at Motive Phosphene Behavior

Transcranial magnetic stimulation (TMS) is a non-invasive neurostimulatory and neuromodulatory technique that can transiently or lastingly modulate cortical excitability (either increasing or decreasing it) via the application of localized magnetic field pulses.1,2 Within the field of TMS, the term state dependency refers to the initial, baseline condition of the particular neural region targeted for stimulation. As can be inferred, the effects of TMS can (and do) vary according to this primary susceptibility and responsiveness of the targeted cortical area.3,4,5

In this experiment, we will examine this concept of state dependency through the elicitation and subjective experience of motive phosphenes. Phosphenes are visually perceived flashes of small lights triggered by electromagnetic pulses to the visual cortex. These small lights can assume varied characteristics depending upon which type of visual cortex is being stimulated. In this particular study, we will be targeting motive phosphenes as elicited through the stimulation of V1/V2 and the V5/MT+ complex visual regions.6

In this article, we examine the effects of visually relevant state dependency on TMS induced motive phosphenic presentations.

Transcranial magnetic stimulation (TMS) is a non-invasive neurostimulatory and neuromodulatory technique that can transiently or lastingly modulate ...

Multiciliated ependymal cells line the ventricles in the adult brain. Abnormal function or structure of ependymal cilia is associated with various neurological deficits. The current ex vivo live imaging of motile ependymal cilia technique allows for a detailed study of ciliary dynamics following several steps. These steps include: mice euthanasia with carbon dioxide according to protocols of The University of Toledo&#8217;s Institutional Animal Care and Use Committee (IACUC); craniectomy followed by brain removal and sagittal brain dissection with a vibratome or sharp blade to obtain very thin sections through the brain lateral ventricles, where the ependymal cilia can be visualized. Incubation of the brain&#8217;s slices in a customized glass-bottom plate containing Dulbecco&#8217;s Modified Eagle&#8217;s Medium (DMEM)/High-Glucose at 37 &#176;C in the presence of 95%/5% O2/CO2 mixture is essential to keep the tissue alive during the experiment. A video of the cilia beating is then recorded using a high-resolution differential interference contrast microscope. The video is then analyzed frame by frame to calculate the ciliary beating frequency. This allows distinct classification of the ependymal cells into three categories or types based on their ciliary beating frequency and angle. Furthermore, this technique allows the use of high-speed fluorescence imaging analysis to characterize the unique intracellular calcium oscillation properties of ependymal cells as well as the effect of pharmacological agents on the calcium oscillations and the ciliary beating frequency. In addition, this technique is suitable for immunofluorescence imaging for ciliary structure and ciliary protein localization studies. This is particularly important in disease diagnosis and phenotype studies. The main limitation of the technique is attributed to the decrease in live motile cilia movement as the brain tissue starts to die.

Using high-resolution differential interference contrast (DIC) microscopy, an ex vivo observation of the beating of motile ependymal cilia located within the mouse brain ventricles is demonstrated by live-imaging. The technique allows a recording of the unique ciliary beating frequency and beating angle as well as their intracellular calcium oscillation pacing properties.

Multiciliated ependymal cells line the ventricles in the adult brain. Abnormal function or structure of ependymal cilia is associated with various ...

Modification of a Colliculo-thalamocortical Mouse Brain Slice, Incorporating 3-D printing of Chamber Components and Multi-scale Optical Imaging

The ability of the brain to process sensory information relies on both ascending and descending sets of projections. Until recently, the only way to study these two systems and how they interact has been with the use of in vivo preparations. Major advances have been made with acute brain slices containing the thalamocortical and cortico-thalamic pathways in the somatosensory, visual, and auditory systems. With key refinements to our recent modification of the auditory thalamocortical slice1, we are able to more reliably capture the projections between most of the major auditory midbrain and forebrain structures: the inferior colliculus (IC), medial geniculate body (MGB), thalamic reticular nucleus (TRN), and the auditory cortex (AC). With portions of all these connections retained, we are able to answer detailed questions that complement the questions that can be answered with in vivo preparations. The use of flavoprotein autofluorescence imaging enables us to rapidly assess connectivity in any given slice and guide the ensuing experiment. Using this slice in conjunction with recording and imaging techniques, we are now better equipped to understand how information processing occurs at each point in the auditory forebrain as information ascends to the cortex, and the impact of descending cortical modulation. 3-D printing to build slice chamber components permits double-sided perfusion and broad access to networks within the slice and maintains the widespread connections key to fully utilizing this preparation.

Using multiple angles to cut the mouse pup brain, we improve upon a previously-described acute brain slice which captures the connections between most of the major auditory midbrain and forebrain structures.

The ability of the brain to process sensory information relies on both ascending and descending sets of projections. Until recently, the only way to study ...

Large-scale Three-dimensional Imaging of Cellular Organization in the Mouse Neocortex

The mammalian neocortex is composed of many types of excitatory and inhibitory neurons, each with specific electrophysiological and biochemical properties, synaptic connections, and in vivo functions, but their basic functional and anatomical organization from cellular to network scale is poorly understood. Here we describe a method for the three-dimensional imaging of fluorescently-labeled neurons across large areas of the brain for the investigation of the cortical cellular organization. Specific types of neurons are labeled by the injection of fluorescent retrograde neuronal tracers or expression of fluorescent proteins in transgenic mice. Block brain samples, e.g., a hemisphere, are prepared after fixation, made transparent with tissue clearing methods, and subjected to fluorescent immunolabeling of the specific cell types. Large areas are scanned using confocal or two-photon microscopes equipped with large working distance objectives and motorized stages. This method can resolve the periodic organization of the cell type-specific microcolumn functional modules in the mouse neocortex. The procedure can be useful for the study of three-dimensional cellular architecture in the diverse brain areas and other complex tissues.

Here we describe a procedure for tissue clearing, fluorescent labeling, and large-scale imaging of mouse brain tissue which, thereby, enables visualization of the three-dimensional organization of cell types in the neocortex.

The mammalian neocortex is composed of many types of excitatory and inhibitory neurons, each with specific electrophysiological and biochemical ...

Wide-field single photon voltage-sensitive dye (VSD) imaging of brain slice preparations is a useful tool to assess the functional connectivity in neural circuits. Due to the fractional change in the light signal, it has been difficult to use this method as a quantitative assay. This article describes special optics and slice handling systems, which render this technique stable and reliable. The present article demonstrates the slice handling, staining, and recording of the VSD-stained hippocampal slices in detail. The system maintains physiological conditions for a long time, with good staining, and prevents mechanical movements of the slice during the recordings. Moreover, it enables staining of slices with a small amount of the dye. The optics achieve high numerical aperture at low magnification, which allows recording of the VSD signal at the maximum frame rate of 10 kHz, with 100 pixel x 100-pixel spatial resolution. Due to the high frame rate and spatial resolution, this technique allows application of the post-recording filters that provide sufficient signal-to-noise ratio to assess the changes in neural circuits.

We introduce a reproducible and stable optical recording method for brain slices using voltage-sensitive dye. The article describes voltage-sensitive dye staining and recording of optical signals using conventional hippocampal slice preparations.

Wide-field single photon voltage-sensitive dye (VSD) imaging of brain slice preparations is a useful tool to assess the functional connectivity in neural ...

Real-Time fMRI Brain Mapping in Animals

Dynamic fMRI responses vary largely according to the physiological conditions of animals either under anesthesia or in awake states. We developed a real-time fMRI platform to guide experimenters to monitor fMRI responses instantaneously during acquisition, which can be used to modify the physiology of animals to achieve desired hemodynamic responses in animal brains. The real-time fMRI set-up is based on a 14.1T preclinical MRI system, enabling the real-time mapping of dynamic fMRI responses in the primary forepaw somatosensory cortex (FP-S1) of anesthetized rats. Instead of a retrospective analysis to investigate confounding sources leading to the variability of fMRI signals, the real-time fMRI platform provides a more effective scheme to identify dynamic fMRI responses using customized macro-functions and a common neuroimage analysis software in the MRI system. Also, it provides immediate troubleshooting feasibility and a real-time biofeedback stimulation paradigm for brain functional studies in animals.

Animal brain functional mapping can benefit from the real-time functional magnetic resonance imaging (fMRI) experimental set-up. Using the latest software implemented in the animal MRI system, we established a real-time monitoring platform for small animal fMRI.

Dynamic fMRI responses vary largely according to the physiological conditions of animals either under anesthesia or in awake states. We developed a ...

Activity of Posterior Lateral Line Afferent Neurons during Swimming in Zebrafish

Sensory systems gather cues essential for directing behavior, but animals must decipher what information is biologically relevant. Locomotion generates reafferent cues that animals must disentangle from relevant sensory cues of the surrounding environment. For example, when a fish swims, flow generated from body undulations is detected by the mechanoreceptive neuromasts, comprising hair cells, that compose the lateral line system. The hair cells then transmit fluid motion information from the sensor to the brain via the sensory afferent neurons. Concurrently, corollary discharge of the motor command is relayed to hair cells to prevent sensory overload. Accounting for the inhibitory effect of predictive motor signals during locomotion is, therefore, critical when evaluating the sensitivity of the lateral line system. We have developed an in vivo electrophysiological approach to simultaneously monitor posterior lateral line afferent neuron and ventral motor root activity in zebrafish larvae (4-7 days post fertilization) that can last for several hours. Extracellular recordings of afferent neurons are achieved using the loose patch clamp technique, which can detect activity from single or multiple neurons. Ventral root recordings are performed through the skin with glass electrodes to detect motor neuron activity. Our experimental protocol provides the potential to monitor endogenous or evoked changes in sensory input across motor behaviors in an intact, behaving vertebrate.

We describe a protocol to monitor changes in the afferent neuron activity during motor commands in a model vertebrate hair cell system.

Sensory systems gather cues essential for directing behavior, but animals must decipher what information is biologically relevant. Locomotion generates ...

Imaging neuronal activities at single-cell resolution in awake behaving animals is a very powerful approach for the investigation of neural circuit functions in systems neuroscience. However, high absorbance and scattering of light in mammalian tissue limit intravital imaging mostly to superficial brain regions, leaving deep-brain areas, such as the hippocampus, out of reach for optical microscopy. In this video, we show the preparation and implantation of the custom-made imaging window to enable chronic in vivo imaging of the dorsal hippocampal CA1 region in head-fixed behaving mice. The custom-made window is supplemented with an infusion cannula that allows targeted delivery of viral vectors and drugs to the imaging area. By combining this preparation with wide-field imaging, we performed a long-term recording of neuronal activity using a fluorescent calcium indicator from large subsets of neurons in behaving mice over several weeks. We also demonstrated the applicability of this preparation for voltage imaging with single-spike resolution. High-performance genetically encoded indicators of neuronal activity and scientific CMOS cameras allowed the recurrent visualization of subcellular morphological details of single neurons at high temporal resolution. We also discuss the advantages and potential limitations of the described method and its compatibility with other imaging techniques.

This article demonstrates the preparation of a custom-made imaging window supplemented with infusion cannula and its implantation onto the CA1 region of the hippocampus in mice.

Imaging neuronal activities at single-cell resolution in awake behaving animals is a very powerful approach for the investigation of neural circuit ...

Wide-field calcium imaging from the mouse&#39;s neocortex allows one to observe cortex-wide neural activity related to various brain functions. On the other hand, two-photon imaging can resolve the activity of local neural circuits at the single-cell level. It is critical to make a large cranial window to perform multiple-scale analysis using both imaging techniques in the same mouse. To achieve this, one must remove a large section of the skull and cover the exposed cortical surface with transparent materials. Previously, glass skulls and polymer-based cranial windows have been developed for this purpose, but these materials are not easily fabricated. The present protocol describes a simple method for making a large cranial window consisting of commercially available polyvinylidene chloride (PVDC) wrapping film, a transparent silicone plug, and a cover glass. For imaging the dorsal surface of an entire hemisphere, the window size was approximately 6 x 3 mm2. Severe brain vibrations were not observed regardless of such a large window. Importantly, the condition of the brain surface did not deteriorate for more than one month. Wide-field imaging of a mouse expressing a genetically-encoded calcium indicator (GECI), GCaMP6f, specifically in astrocytes, revealed synchronized responses in a few millimeters. Two-photon imaging of the same mouse showed prominent calcium responses in individual astrocytes over several seconds. Furthermore, a thin layer of an adeno-associated virus was applied to the PVDC film and successfully expressed GECI in cortical neurons over the cranial window. This technique is reliable and cost-effective for making a large cranial window and facilitates the investigation of the neural and glial dynamics and their interactions during behavior at the macroscopic and microscopic levels.

The present protocol describes making a large (6 x 3 mm2) cranial window using food wrap, transparent silicone, and cover glass. This cranial window allows in vivo wide-field and two-photon calcium imaging experiments in the same mouse.

Wide-field calcium imaging from the mouse&#39;s neocortex allows one to observe cortex-wide neural activity related to various brain functions. On the ...

Two-Photon and Wide-Field Calcium Imaging in the Superior Colliculus

Calcium Imaging in Mouse Superior Colliculus

The superior colliculus (SC), an evolutionarily conserved midbrain structure in all vertebrates, is the most sophisticated visual center before the emergence of the cerebral cortex. It receives direct inputs from ~30 types of retinal ganglion cells (RGCs), with each encoding a specific visual feature. It remains elusive whether the SC simply inherits retinal features or if additional and potentially de novo processing occurs in the SC. To reveal the neural coding of visual information in the SC, we provide here a detailed protocol to optically record visual responses with two complementary methods in awake mice. One method uses two-photon microscopy to image calcium activity at single-cell resolution without ablating the overlaying cortex, while the other uses wide-field microscopy to image the whole SC of a mutant mouse whose cortex is largely undeveloped. This protocol details these two methods, including animal preparation, viral injection, headplate implantation, plug implantation, data acquisition, and data analysis. The representative results show that the two-photon calcium imaging reveals visually evoked neuronal responses at single-cell resolution, and the wide-field calcium imaging reveals&#160;neural activity across the entire SC. By combining these two methods, one can reveal the neural coding in the SC at different scales, and such combination can also be applied to other brain regions.

Author Spotlight: Unveiling Neural Coding and Mechanisms of Visual Processing in the Superior Colliculus 

This protocol details the procedure for imaging calcium responses in the superior colliculus (SC) of awake mice, including imaging single-neuron activity with two-photon microscopy while leaving the cortex intact in wild-type mice, and imaging the entire SC with wide-field microscopy in partial-cortex mutant mice.

The superior colliculus (SC), an evolutionarily conserved midbrain structure in all vertebrates, is the most sophisticated visual center before the ...