This work was supported by the Institute of Molecular Biology, Academia Sinica, and National Science and Technology Council, Taiwan. The Machine Shop at the Institute of Physics, Academia Sinica helped to fabricate custom-designed parts. We also want to thank P. Argast (Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland) for the design of the quick-lock mechanism of the head stage.

All animal procedures were approved and carried out in accordance with the guidelines of the Institutional Animal Care and Use Committee of Academia Sinica. Details of the research tools can be found in the Table of Materials.
1. Preparation of recording chamber
<ol>
	<li>Prepare a semi-hexagonal tank, a base plate, and a head stage (Figure 1A; Supplementary Files 1-3). The head stage consists of two metal posts...

Behavior Tracking and Neural Activity Pattern in the Zebrafish Forebrain

<ol>
	<li>Grienberger, C., Konnerth, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+calcium+in+neurons.">Imaging calcium in neurons.</a> Neuron. 73 (5), 862-885 (2012).</li><li>Chow, D. M., 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=Deep+three-photon+imaging+of+the+brain+in+intact+adult+zebrafish.">Deep three-photon imaging of the brain in intact adult zebrafish.</a> Nature Methods. 17 (6), 605-608 (2020).</li><li>Mittmann, W., 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=Two-photon+calcium+imaging+of+evoked+activity+from+L5+somatosensory+neurons+in+vivo.">Two-photon calcium imaging of evoked activity from L5 somatosensory neurons in vivo.</a> Nature Neuroscience. 14 (8), 1089-1093 (2011).</li><li>Friedrich, R. W., Jacobson, G. A., Zhu, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Circuit+neuroscience+in+zebrafish.">Circuit neuroscience in zebrafish.</a> Current Biology. 20 (8), R371-R381 (2010).</li><li>Kappel, J. M., 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=Visual+recognition+of+social+signals+by+a+tectothalamic+neural+circuit.">Visual recognition of social signals by a tectothalamic neural circuit.</a> Nature. 608 (7921), 146-152 (2022).</li><li>Bartoszek, E. M., 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=Ongoing+habenular+activity+is+driven+by+forebrain+networks+and+modulated+by+olfactory+stimuli.">Ongoing habenular activity is driven by forebrain networks and modulated by olfactory stimuli.</a> Current Biology. 31 (17), 3861-3874 (2021).</li><li>Valente, A., Huang, K. H., Portugues, R., Engert, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ontogeny+of+classical+and+operant+learning+behaviors+in+zebrafish.">Ontogeny of classical and operant learning behaviors in zebrafish.</a> Learning &amp; Memory. 19 (4), 170-177 (2012).</li><li>Buske, C., Gerlai, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Maturation+of+shoaling+behavior+is+accompanied+by+changes+in+the+dopaminergic+and+serotoninergic+systems+in+zebrafish.">Maturation of shoaling behavior is accompanied by changes in the dopaminergic and serotoninergic systems in zebrafish.</a> Developmental Psychobiology. 54 (1), 28-35 (2012).</li><li>Huang, K. 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=A+virtual+reality+system+to+analyze+neural+activity+and+behavior+in+adult+zebrafish.">A virtual reality system to analyze neural activity and behavior in adult zebrafish.</a> Nature Methods. 17 (3), 343-351 (2020).</li><li>Rupprecht, P., Prendergast, A., Wyart, C., Friedrich, R. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Remote+z-scanning+with+a+macroscopic+voice+coil+motor+for+fast+3D+multiphoton+laser+scanning+microscopy.">Remote z-scanning with a macroscopic voice coil motor for fast 3D multiphoton laser scanning microscopy.</a> Biomedical Optics Express. 7 (5), 1656-1671 (2016).</li><li>Papadopoulos, I. N., Jouhanneau, J. -. S., Poulet, J. F. A., Judkewitz, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Scattering+compensation+by+focus+scanning+holographic+aberration+probing+(F-SHARP).">Scattering compensation by focus scanning holographic aberration probing (F-SHARP).</a> Nature Photonics. 11 (2), 116-123 (2017).</li><li>Torigoe, M., 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=Zebrafish+capable+of+generating+future+state+prediction+error+show+improved+active+avoidance+behavior+in+virtual+reality.">Zebrafish capable of generating future state prediction error show improved active avoidance behavior in virtual reality.</a> Nature Communications. 12 (1), 5712 (2021).</li></ol>

Here, we describe a detailed protocol to restrain the head of adult zebrafish for two-photon calcium imaging. There are two critical steps to achieve a head restraint that is stable enough for laser scanning imaging. First, the head bar has to be glued to the specific attachment sites of the skulls. Other parts of the skull&#160;are often too thin to provide mechanical stability and may even be fractured during strong body movements. Second, the skin above the attachment sites has to be thoroughly removed. Residual water...

Calcium fluorescence imaging with genetically encoded indicators or synthetic dyes has been a powerful method of measuring neuronal activity in behaving animals, including non-human primates, rodents, birds, and insects1. The activity of hundreds of cells, up to approximately 800 &#181;m below the brain surface, can be measured simultaneously using multi-photon imaging2,3. The activity of specific cell types can also be measured by expressing calcium indicators in genetically defined neuronal populations. Application of the imaging method for small vertebrate models opens up new possibilities in the field of neuronal computation across brain regions.
Zebrafish are a widely used model system in neuroscience research. Larval zebrafish at around 6 days post-fertilization have been used for calcium imaging due to their miniature brain and transparent body4. Juvenile zebrafish (3-4 weeks old) are also used for studying the neural mechanisms underlying sensorimotor pathways5,6. However, the maximal performance level for complex behaviors, including associative learning and social behaviors, is reached at an older age7,8. Thus, a reliable protocol is required to study multiple cognitive functions in the brains of adult zebrafish using imaging methods. While zebrafish larva and juvenile zebrafish can be embedded in agarose for in vivo imaging, adult zebrafish at 2 months or older suffer from hypoxia in such conditions and are physically too strong to be restrained by agarose. Therefore, a surgical procedure is required to stabilize the brain and enable the animal to breathe freely through the gills. 
Here, we describe a head restraint protocol that involves a novel design of a single head bar. The reduced surgery time of 25 min is twice as fast as the previous method9. We also describe the design of the recording chamber (semi-hexagonal tank), the head stage and a quick-lock mechanism to combine the two parts9. Finally, the setup to present an immersive visual stimulus to study visually triggered brain activity and behaviors is also described. Overall, the procedures described here can be used to perform two-photon calcium imaging in genetically defined cell populations in a head-restrained adult zebrafish, enabling the investigation of brain activities during various behavioral paradigms.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Acquisition card</td>
			<td>MBF Bioscience</td>
			<td>Vidrio vDAQ</td>
			<td>Microscope</td>
		</tr>
		<tr>
			<td>Back-projection film</td>
			<td>Kimoto</td>
			<td>Diland screen - GSK</td>
			<td>present visual stimulus</td>
		</tr>
		<tr>
			<td>Band-pass filter (510/80 nm)</td>
			<td>Chroma</td>
			<td>ET510/80m</td>
			<td>Microscope</td>
		</tr>
		<tr>
			<td>Base plate for the semi-hexagonal tank</td>
			<td>custom made</td>
			<td>see supplemental files</td>
			<td>recording chamber</td>
		</tr>
		<tr>
			<td>Camera filter (&#60;875 nm)</td>
			<td>Edmund optics</td>
			<td>#86-106</td>
			<td>Behavior recording</td>
		</tr>
		<tr>
			<td>Camera filter (&#62;700 nm)</td>
			<td>Edmund optics</td>
			<td>#43-949</td>
			<td>Behavior recording</td>
		</tr>
		<tr>
			<td>Camera lens</td>
			<td>Thorlabs</td>
			<td>MVL50M23</td>
			<td>Behavior recording</td>
		</tr>
		<tr>
			<td>Chameleon Vision-S</td>
			<td>Coherent</td>
			<td>Vision-S</td>
			<td>Laser</td>
		</tr>
		<tr>
			<td>Circular plate for the head stage</td>
			<td>custom made</td>
			<td>see supplemental files</td>
			<td>recording chamber</td>
		</tr>
		<tr>
			<td>Controller for piezo actuator</td>
			<td>Physik Instrumente&#160;</td>
			<td>E-665. CR</td>
			<td>Microscope</td>
		</tr>
		<tr>
			<td>Current amplifier</td>
			<td>Thorlabs</td>
			<td>TIA60</td>
			<td>Microscope</td>
		</tr>
		<tr>
			<td>Elitedent Q-6</td>
			<td>Rolence Enterprise</td>
			<td>Q-6</td>
			<td>Surgery: UV lamp</td>
		</tr>
		<tr>
			<td>Emission Filter 510/80 nm</td>
			<td>Chroma</td>
			<td>ET510/80m</td>
			<td>Microscope</td>
		</tr>
		<tr>
			<td>Head bar</td>
			<td>custom made</td>
			<td>see supplemental files</td>
			<td>recording chamber</td>
		</tr>
		<tr>
			<td>Infrared light</td>
			<td>Thorlabs</td>
			<td>M810L3</td>
			<td>Behavior recording</td>
		</tr>
		<tr>
			<td>LED projector</td>
			<td>AAXA</td>
			<td>P2B LED Pico Projector</td>
			<td>present visual stimulus</td>
		</tr>
		<tr>
			<td>Moist paper tissue (Kimwipe)</td>
			<td>Kimtech Science</td>
			<td>34155</td>
			<td>Surgery: moist paper tissue</td>
		</tr>
		<tr>
			<td>Motorized XY sample stage</td>
			<td>Zaber</td>
			<td>X-LRM050</td>
			<td>Microscope</td>
		</tr>
		<tr>
			<td>Neutral Density Filters (50% Transmission)</td>
			<td>Thorlabs</td>
			<td>NE203B</td>
			<td>present visual stimulus</td>
		</tr>
		<tr>
			<td>&#216;1/2&#34; Post Holder</td>
			<td>ThorLabs</td>
			<td>PH1.5V</td>
			<td>Surgery: hollow tube for cannon</td>
		</tr>
		<tr>
			<td>&#216;1/2&#34; Stainless Steel Optical Post</td>
			<td>ThorLabs</td>
			<td>TR150/M</td>
			<td>Surgery: fish loading module</td>
		</tr>
		<tr>
			<td>Objective lens 16x, 0.8NA</td>
			<td>Nikon</td>
			<td>CF175</td>
			<td>Microscope</td>
		</tr>
		<tr>
			<td>Oil-based modeling clay</td>
			<td>Ly Hsin Clay</td>
			<td>C4086</td>
			<td>Surgery: head bar holder</td>
		</tr>
		<tr>
			<td>Optical adhesive</td>
			<td>Norland Products</td>
			<td>NOA68</td>
			<td>Surgery: UV curable glue</td>
		</tr>
		<tr>
			<td>Photomultiplier tube</td>
			<td>Hamamatsu</td>
			<td>H11706P-40</td>
			<td>Microscope</td>
		</tr>
		<tr>
			<td>Piezo actuator</td>
			<td>Physik Instrumente&#160;</td>
			<td>P-725.4CA PIFOC</td>
			<td>Microscope</td>
		</tr>
		<tr>
			<td>Pockels Cell</td>
			<td>Conoptics</td>
			<td>M350-80-LA-BK-02</td>
			<td>Microscope</td>
		</tr>
		<tr>
			<td>Red Wratten filter (&#62; 600 nm)</td>
			<td>Edmund optics</td>
			<td>#53-699</td>
			<td>present visual stimulus</td>
		</tr>
		<tr>
			<td>Resonant-Galvo Scan System</td>
			<td>INSS</td>
			<td>RGE-02</td>
			<td>Microscope</td>
		</tr>
		<tr>
			<td>Right-Angle Clamp for &#216;1/2&#34; Post</td>
			<td>ThorLabs</td>
			<td>RA90/M</td>
			<td>Surgery: fish loading module</td>
		</tr>
		<tr>
			<td>Rotating Clamp for &#216;1/2&#34; Post</td>
			<td>ThorLabs</td>
			<td>SWC/M</td>
			<td>Surgery: fish loading module</td>
		</tr>
		<tr>
			<td>ScanImage</td>
			<td>MBF Bioscience</td>
			<td>Basic version</td>
			<td>Microscope</td>
		</tr>
		<tr>
			<td>Semi-hexagonal tank</td>
			<td>custom made</td>
			<td>see supplemental files</td>
			<td>recording chamber</td>
		</tr>
		<tr>
			<td>Super-Bond C&#38;B Kit</td>
			<td>Sun Medical Co.</td>
			<td>Super-Bond C&#38;B</td>
			<td>Surgery: dental cement</td>
		</tr>
		<tr>
			<td>Tricaine methanesulfonate</td>
			<td>Sigma Aldrich</td>
			<td>E10521</td>
			<td>Surgery: anesthetic</td>
		</tr>
		<tr>
			<td>USB Camera</td>
			<td>FLIR</td>
			<td>BFS-U3-13Y3M-C</td>
			<td>Behavior recording</td>
		</tr>
		<tr>
			<td>Vetbond</td>
			<td>3M</td>
			<td>1469SB</td>
			<td>Surgery: tissue glue</td>
		</tr>
	</tbody>
</table>

two-photon calcium imaging of forebrain activity in behaving adult zebrafish

Adult zebrafish (Danio rerio) exhibit a rich repertoire of behaviors for studying cognitive functions. They also have a miniature brain that can be used for measuring activities across brain regions through optical imaging methods. However, reports on the recording of brain activity in behaving adult zebrafish have been scarce. The present study describes procedures to perform two-photon calcium imaging in the dorsal forebrain of adult zebrafish. We focus on steps to restrain adult zebrafish from moving their heads, which provides stability that enables laser scanning imaging of the brain activity. The head-restrained animals can freely move their body parts and breathe without aids. The procedure aims to shorten the time of head restraint surgery, minimize brain motion, and maximize the number of neurons recorded. A setup for presenting an immersive visual environment during calcium imaging is also described here, which can be used to study neural correlates underlying visually triggered behaviors.

Two-Photon Calcium Imaging of Forebrain Activity in Behaving Adult Zebrafish

The protocol consists of two parts: head restraint surgery and two-photon calcium imaging of neuronal activities in the forebrain. The success of surgery is defined by the survival of the animal and the stability of the head restraint. The survival rate can be greatly improved by frequent perfusion of 0.01% TMS solution through the mouth during surgery. Fish should recover from anesthesia and breathe actively within 1-2 min after being immersed into fish tank water. Two-photon calcium imaging enables activity recording o...

Watch this Scientific Journal Video about Advancements in Adult Zebrafish Brain Research at JoVE.com

Advancements in Adult Zebrafish Brain Research (Video) | JoVE

Here, we present a protocol to perform two-photon calcium imaging in the dorsal forebrain of adult zebrafish.

Adult zebrafish (Danio rerio) exhibit a rich repertoire of behaviors for studying cognitive functions. They also have a miniature brain that can be used ...