Thank you to Willy Sun for technical assistance and Dr. Kris Gellynck for helpful comments and three anonymous reviewers for their constructive advice. This work was funded by the Sunnybrook Hearing Regeneration Initiative

Mouse tissue was harvested from Sox2EGFP-reporter mice12 maintained and euthanized in accordance with Canadian Council on Animal Care guidelines for the care and use of laboratory animals.
1. Culturing Embryonic Cochleae
<ol>
	<li>Supplement Dulbecco&#8217;s Modified Eagle Medium (DMEM) by mixing 8.89 ml of DMEM, 1 ml of fetal bovine serum (FBS), 100 &#956;l of 100x N2 supplement, and 10 &#956;l of 10 mg/ml ciprofloxacin. Supplement Hank&#8217;s Balanced Salt Solution (HBSS) by mixing 495 ml HBSS with 5 ml of 100% HEPES.</li>
	<li>Prepare glass bottom culture dishes:
	<ol>
		<li>In a laminar flow hood, resuspend 200 &#181;l basement membrane extract substrate in 5 ml DMEM. Prepare 35 mm diameter glass bottom culture dishes with 10 mm wells. Pipette 150 &#181;l substrate/DMEM in to the center of each glass bottomed dish. These dishes can be used after 40 min incubation, or can stored in a CO2 incubator at 35 &#176;C for at least a week. 
		NOTE: Glass bottomed dishes are used for the following reasons: to ensure that the base of the dish is transparent and suitable for imaging, to create a well in the center of the dish that allows the explants to settle in an easily located area and finally so that after an experiment the sample can be processed for immunostaining and subsequent analysis.</li>
	</ol>
	</li>
	<li>Prepare the work-station and tools:
	<ol>
		<li>Turn on the laminar flow clean bench, and spray down with 70% EtOH to create a clean work space. Soak forceps, spoons, and a black 184 silicone elastomer dish (a mix of 184 silicone elastomer (10 parts), curing agent (1 part) and charcoal powder (2.5 g)) in 70% EtOH.</li>
	</ol>
	</li>
	<li>In the clean work station, harvest embryos for the experiment. Collect embryos of the appropriate gestation in ice cold HBSS supplemented with 1% HEPES.
	<ol>
		<li>Determine an external or visible organ that will demonstrate reporter activity and examine the embryos using a fluorescent stereo microscope. Collect the embryos that exhibit reporter activity in ice cold HBSS supplemented with 1% HEPES as these are the subject of the experiment.</li>
	</ol>
	</li>
	<li>Collect temporal bones:
	<ol>
		<li>Working quickly, using a cool light source and fine forceps, collect the heads of the pups. Take care to clip at the cervical vertebrae and below the jaw to avoid damage to the temporal bones.</li>
		<li>Carefully open the skull. Remove the brain, trim off the front of the head, and transfer the posterior skull to fresh ice cold HBSS supplemented with 1% HEPES in a clean dish. Carefully dissect out the peanut shaped temporal bones taking care to keep the vestibular system in tact.</li>
	</ol>
	</li>
	<li>Dissect the cochlea:
	<ol>
		<li>Transfer the temporal bones to a black silicone elastomer coated dish in ice cold HBSS supplemented with 1% HEPES, pin the vestibular region of the bone. Insert insect pins at an oblique angle in order to stabilize the temporal bone and create room for the forceps. Pinning is a crucial step in the process as if the temporal bone is allowed to move too much it is very difficult to harvest an intact cochlea.</li>
		<li>Carefully remove the cartilage surrounding the cochlea. Insert one tine of the forceps into the cartilage at the outer edge of the base of the cochlea and clip a hole into the cartilage.</li>
		<li>Clip a flap up the side, insert the tine of the forceps and gently separate the roof of the duct from the cartilage. Clip horizontally across the top and diagonally, and carefully lift off the front section of the capsule. Insert a prong of the forceps in between the remaining cartilage and the duct and gently clip off the last section. The apical surface of the cochlea is now exposed.</li>
		<li>Starting at the base, catch the area where the roof of the duct meets the cochlear epithelium and open the cochlear duct. Gently peel off the roof, trimming when necessary until it is completely removed. Trim off any portions of membrane left on the medial side of the duct. Clean the duct of excess mesenchymal tissue and detach the duct from the vestibular system.</li>
	</ol>
	</li>
	<li>Culture the explants:
	<ol>
		<li>Place an explant, luminal surface up, in the center of a substrate coated glass bottom culture dish, carefully draw off all of the liquid and leave for two minutes. Add 150 &#181;l supplemented DMEM drop-wise to the explant, taking care not to disturb it. Should the explant float free, reposition with forceps, but take care that the explant settles to the bottom of the dish so that it can attach to the substrate.</li>
		<li>Place the glass bottom dishes in a deep 12 cm diameter Petri dish, with a small dish of sterile water to maintain humidity. Put the cultures in to a 35 &#176;C incubator overnight in order for the explant to attach to the substrate and flatten.</li>
	</ol>
	</li>
</ol>
2. Live Imaging
<ol>
	<li>Select explant samples. Use a fluorescent stereo microscope to evaluate the condition of each explanted cochlea. Only select explants where the duct is intact and attached to the glass from base to apex.</li>
	<li>Set the incubator at 35 &#176;C with 5% CO2 to culture cochlear tissue. Put the cultures into the incubator microscope:
	<ol>
		<li>Gently aspirate off the supplemented DMEM and replace with at least 500 &#956;l fresh media. For imaging up to 6 days, 1-1.5 ml is better. In cases where explants are loosely attached, pipette a ring of media around the edge of the dish. This extra liquid will make a miniature &#8216;humidified chamber&#8217; without disturbing the explant while it continues to attach to the matrix.
		<ol>
			<li>Alternatively, use hinged dish covers to open the lids while the dish stays in its fitting in the microscope if reagents need to be exchanged during intervals between image collections. Hinged dish covers allow the lids to be opened without disturbing the samples or removing the dishes from their settings. This maintains their exact position for subsequent image captures.</li>
		</ol>
		</li>
		<li>Insert the glass bottom dishes containing appropriate samples into the sample dish holder. The microscope in this example has a rotating platform that holds eight 35 mm sample dishes.</li>
		<li>Under the laminar flow hood replace the plastic lids with glass lids and insert the dishes into the sample dish holder. Place the sample dish holder inside the incubator taking care not to dislodge the explants from the bottom of the dish or to disturb the media.</li>
	</ol>
	</li>
	<li>Set up the imaging routine:
	<ol>
		<li>Switch on the microscope, UV lamp and camera and open the imaging software.</li>
		<li>Locate the samples, pick an imaging area, plane of focus and adjust exposure times for each dish in sequence. Choose the plane of focus depending not only on the view of the explant at the time of starting, but also bearing in mind how the tissue will move and how long the time course will run.</li>
		<li>Set a Z stack centering around the selected focal plane in the fluorescence channel. Set the frequency and length of the sampling for the experiment. The frequency of sampling will be limited by the time it takes to collect images, so this should be determined after selecting fields of view and setting a Z stack. In this case sampling takes place every 30 min over five days. The duration of the experiment can be up to 14 days.</li>
	</ol>
	</li>
	<li>Generate a movie:
	<ol>
		<li>At the end of the time lapse period open the image files. In this case Metamorph software that opens sequential collection points is used. Frame by frame pick the best focal plane for showing the cell population of interest.</li>
		<li>Convert these images to an .avi file, or export them as a montage to generate a set of images that can be opened and analyzed in image processing software or converted to multiple formats using video processing software.</li>
	</ol>
	</li>
</ol>

<ol>
	<li>Wu, D. K., Kelley, M. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+mechanisms+of+inner+ear+development.">Molecular mechanisms of inner ear development.</a> Cold Spring Harbor perspectives in biology. 4, (2012).</li><li>Shim, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+auditory+sensory+epithelium:+the+instrument+of+sound+perception.">The auditory sensory epithelium: the instrument of sound perception.</a> The international journal of biochemistry &amp; cell biology. 38, 1827-1833 (2006).</li><li>Van de Water, T., Ruben, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Growth+of+the+inner+ear+in+organ+culture.">Growth of the inner ear in organ culture.</a> The Annals of otology, rhinology, and laryngology. 83, 1-16 (1974).</li><li>Jacques, B. E., 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+dual+function+for+canonical+Wnt/beta-catenin+signaling+in+the+developing+mammalian+cochlea.">A dual function for canonical Wnt/beta-catenin signaling in the developing mammalian cochlea.</a> Development. 139, 4395-4404 (2012).</li><li>Castellano-Munoz, M., Peng, A. W., Salles, F. T., Ricci, A. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Swept+field+laser+confocal+microscopy+for+enhanced+spatial+and+temporal+resolution+in+live-cell+imaging.+Microscopy+and+microanalysis+:+the+official+journal+of+Microscopy.">Swept field laser confocal microscopy for enhanced spatial and temporal resolution in live-cell imaging. Microscopy and microanalysis : the official journal of Microscopy.</a> Society of America, Microbeam Analysis Society, Microscopical Society of Canada. 18, 753-760 (2012).</li><li>Szarama, K. B., Gavara, N., Petralia, R. S., Chadwick, R. S., Kelley, M. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thyroid+hormone+increases+fibroblast+growth+factor+receptor+expression+and+disrupts+cell+mechanics+in+the+developing+organ+of+corti.">Thyroid hormone increases fibroblast growth factor receptor expression and disrupts cell mechanics in the developing organ of corti.</a> BMC developmental biology. 13, 6 (2013).</li><li>Appler, 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=Gata3+is+a+critical+regulator+of+cochlear+wiring.">Gata3 is a critical regulator of cochlear wiring.</a> The Journal of neuroscience : the official journal of the Society for Neuroscience. 33, 3679-3691 (2013).</li><li>Wibowo, I., Pinto-Teixeira, F., Satou, C., Higashijima, S., Lopez-Schier, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Compartmentalized+Notch+signaling+sustains+epithelial+mirror+symmetry.">Compartmentalized Notch signaling sustains epithelial mirror symmetry.</a> Development. 138, 1143-1152 (2011).</li><li>Hashimoto, S., Kato, N., Saeki, K., Morimoto, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Selection+of+high-potential+embryos+by+culture+in+poly(dimethylsiloxane)+microwells+and+time-lapse+imaging.">Selection of high-potential embryos by culture in poly(dimethylsiloxane) microwells and time-lapse imaging.</a> Fertility and sterility. 97, 332-337 (2012).</li><li>Matsuoka, F., 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=Morphology-based+prediction+of+osteogenic+differentiation+potential+of+human+mesenchymal+stem+cells.">Morphology-based prediction of osteogenic differentiation potential of human mesenchymal stem cells.</a> PloS one. 8, (2013).</li><li>Ma, G. F., 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=et+al.Transforming+growth+factor-beta1+and+-beta2+in+gastric+precancer+and+cancer+and+roles+in+tumor-cell+interactions+with+peripheral+blood+mononuclear+cells+in+vitro.">et al.Transforming growth factor-beta1 and -beta2 in gastric precancer and cancer and roles in tumor-cell interactions with peripheral blood mononuclear cells in vitro.</a> PloS one. 8, (2013).</li><li>Taranova, O. V., 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=SOX2+is+a+dose-dependent+regulator+of+retinal+neural+progenitor+competence.">SOX2 is a dose-dependent regulator of retinal neural progenitor competence.</a> Genes &amp; development. 20, 1187-1202 (2006).</li><li>Chen, P., Segil, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=p27(Kip1)+links+cell+proliferation+to+morphogenesis+in+the+developing+organ+of+Corti.">p27(Kip1) links cell proliferation to morphogenesis in the developing organ of Corti.</a> Development. , 1581-1590 (1999).</li></ol>

The authors have nothing to disclose.

There are several technical points to consider when cultures are established and in setting up the time-lapse microscope in order for long-term imaging.
We use basement membrane matrix as a substrate for culturing cochlear explants, but the substrate should be matched to the cell type. For example, to image neuronal cultures, it may be better to provide a fibronectin coating. Incubation temperature and gas composition should also be chosen according to tissue type. Choosing the age of the expl...

The mammalian cochlea is a highly ordered complex organ. In the mouse, between the emergence of the primitive inner ear from the otic vesicle on day E11 and completion of the developmental program at early postnatal stages, multiple waves of cell signaling and coordinated changes in gene expression take place. Running from base to apex of the cochlear duct is the sound detecting sensory epithelium, or organ of Corti. Development of the organ of Corti is exquisitely controlled such that by the end of development, it will consist of a single row of inner hair cells, three rows of outer hair cells interspersed with five rows of supporting cells (two rows of pillar cells, three rows of Deiters&#8217; cells)1. Deviation from this precise order results in hearing loss, highlighting the importance of study&#160;of the genesis and patterning of the sensory epithelium2.
In vitro culturing of the embryonic mouse cochlea is an essential tool in studying the mechanisms of development of the organ of Corti. This technique was established in 1974 and over the last 40 years, has been used to elucidate many of the mechanisms by which the sensory epithelium is specified and the organ of Corti established3. The cochlea is a complex organ with dynamic developmental processes; a manipulation may take as long as seven days to manifest1. For example, when adding GSK 3&#946; inhibitors to a cochlear explant culture at E13, the optimal incubation period to observe a robust effect of the compound is six days4.
Live imaging of the developing cochlea allows investigation into changes in the morphology of the organ of Corti, changes in gene expression, tracking of migrating, proliferating or dying cells, and it allows real-time observation of the results of pharmaceutical agents and disruption of signaling pathways. Until now, live imaging of the cochlea has mainly been performed using confocal microscopy to image small areas of the organ of Corti over short time periods5-8, but this technique has limitations due to explant viability. In imaging of the effects of longer-term manipulations on slow developmental processes, the imaging environment is crucial. Typically a confocal live imaging system uses a humidified plastic box that sits on the microscope. Heat and humidity can escape through the gaps in the incubating box where it meets the microscope table, through the access windows, through the hinged openings and through the gaps around various parts of the microscope- such as the objective or the light source. This is not optimal for maintaining healthy explants for more than two or three days.
We define &#8216;incubator microscope&#8217; as an inverted microscope sealed inside a standard CO2 incubator, rather than an incubator built around the microscope. An incubator microscope extends the life of the experiment such that rather than imaging over two or three days, samples can be imaged for up to two weeks. An incubator microscope provides an excellent environment for cell growth and differentiation, with minimal disturbance to explant cultures and standard controlled conditions. In studies that take place over multiple days it is common to resort to imaging samples on a daily basis by removing them from the incubator and carrying them to an inverted fluorescent microscope. While this approach can work, removing the dishes from the incubator inflicts stress on the sensitive developing tissue. Changes in acidity of the culturing medium and fluctuations in temperature due to removal from the incubator can result in suboptimal development and unhealthy tissue. Imaging the same region at the same focal plane and in the same orientation at every time point is extremely challenging. By using an automated system within an incubator, it is possible to maintain healthy tissue, to collect images at more time points and to ensure that the same area is captured in every frame. In recent years several integrated microscope tissue incubators have been developed, these have been useful not only in clinical practice9 but also in stem cell and cancer research10,11.
Here we present a protocol for long term live imaging of embryonic mouse cochlear explants. We use an automated microscopy system inside a standard CO2 incubator that has the capability to capture images of multiple samples at set time points. The system consists of an inverted microscope set inside an incubator. Samples are placed in a rotating dais that allows imaging of multiple samples at each time point. Illumination, image capture, and rotation of the dais are controlled by an automated system operated through Metamorph software. By setting an imaging routine using the operating software we can set an experiment to run for up to two weeks with minimal human intervention. In this example we use both bright field and fluorescence to show large-scale growth and rearrangement of the cochlea, and specifically, the prosensory region. In this experiment, cochleae will be dissected from Sox2EGFP reporter mice on embryonic day E13. In vitro cultures will be established and then imaged over five days.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Dulbecco&#39;s Modified Eagle media</td>
			<td>Gibco</td>
			<td>12430</td>
			<td>Multiple brands manufacture this</td>
			<td>http://www.lifetechnologies.com/us/en/home/life-science/cell-culture/mammalian-cell-culture/classical-media/dmem.html</td>
		</tr>
		<tr>
			<td>Basement membrane extract&#160;</td>
			<td>Corning</td>
			<td>354230</td>
			<td>Matrigel. Alternative similar products are available from other suppliers. 
			http://catalog2.corning.com/Lifesciences/en-US/Shopping/Product.aspx?categoryname=Cell+Culture+and+Bioprocess%28Lifesciences%29|Extracellular+Matrix+Proteins+ECMs+and+Attachment+Factors%28Lifesciences%29|Matrigel+Basement+Membrane+Matrix+%28Lifesciences%29</td>
		</tr>
		<tr>
			<td>Fetal bovine serum</td>
			<td>Gibco</td>
			<td>16000044</td>
			<td>Multiple brands manufacture this 
			http://www.lifetechnologies.com/search/global/searchAction.action?query=fbs&#38;resultPage=1&#38;results PerPage=15&#38;autocomplete=</td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Gibco</td>
			<td>5630080</td>
			<td>Multiple brands manufacture this 
			http://www.lifetechnologies.com/search/global/searchAction.action?query=hepes&#38;resultPage=1&#38;results PerPage=15&#38;autocomplete=</td>
		</tr>
		<tr>
			<td>100 x N2 supplement</td>
			<td>Gibco</td>
			<td>17502-048</td>
			<td>Multiple brands manufacture this 
			http://www.lifetechnologies.com/search/global/searchAction.action?query=n2&#38;resultPage=1&#38;results PerPage=15&#38;autocomplete=</td>
		</tr>
		<tr>
			<td>Ciprofloxacin</td>
			<td>Sigma Aldrich</td>
			<td>17850-5G-F</td>
			<td>Multiple brands manufacture this 
			http://www.sigmaaldrich.com/catalog/product/fluka/17850?lang=en&#38;region=CA</td>
		</tr>
		<tr>
			<td>Hank&#39;s balanced salt solution</td>
			<td>Gibco</td>
			<td>14170161</td>
			<td>Multiple brands manufacture this. Should be refidgerated before use. 
			http://www.lifetechnologies.com/us/en/home/life-science/cell-culture/mammalian-cell-culture/reagents/balanced-salt-solutions/hbss-hanks-balanced-salt-solution.html?s_kwcid=AL!3652!3!26107410508!e!!g!!hbss&#38;ef_id=xoFOglw2s UMAAMU8:20140228185720:s</td>
		</tr>
		<tr>
			<td>Fine Forceps</td>
			<td>Fine Science tools</td>
			<td>11254-20</td>
			<td>Size number 5 
			http://www.finescience.ca/Special-Pages/Products.aspx?ProductId=350&#38;CategoryId=29</td>
		</tr>
		<tr>
			<td>Curette&#160;</td>
			<td>Fine Science Tools</td>
			<td>10080-05</td>
			<td>size 1 mm&#160; 
			http://www.finescience.ca/Special-Pages/Products.aspx?ProductId=91&#38;CategoryId=118</td>
		</tr>
		<tr>
			<td>Insect Pins</td>
			<td>Fine Science Tools</td>
			<td>26001-35</td>
			<td>Must be stainless Steel 
			http://www.finescience.ca/Special-Pages/Products.aspx?ProductId=124</td>
		</tr>
		<tr>
			<td>50 mm plastic dishes</td>
			<td>Corning/Falcon</td>
			<td>351006</td>
			<td>Multiple brands manufacture this</td>
		</tr>
		<tr>
			<td>charcoal</td>
			<td>Sigma Aldrich</td>
			<td>05105-250G</td>
			<td>Multiple brands manufacture similar items 
			http://www.sigmaaldrich.com/catalog/product/fluka/05105?lang=en&#38;region=CA</td>
		</tr>
		<tr>
			<td>184 silicone elastomer</td>
			<td>Dow/Corning&#160;</td>
			<td>SYLGARD&#174; 184 SILICONE ELASTOMER KIT</td>
			<td>Dishes are home made several weeks in advance.&#160; Silicone elastomer can be from any supplier.<a href="http://www.dowcorning.com/applications/search/products/Details.aspx?prod=01064291">http://www.dowcorning.com/applications/search/products/Details.aspx?prod=01064291</a></td>
		</tr>
		<tr>
			<td>Glass bottom dishes</td>
			<td>MatTek</td>
			<td>P35G-0-10-C</td>
			<td>The dimensions of the dish are determined by the specifications of the imaging system.&#160; 35 mm diameter, 10mm well, number 0 coverslip fits Olympus Vivaview FL. 
			http://glass-bottom-dishes.com/catalog/index.php?main_page=product_info&#38;cPath= 1_4_15&#38;products_id=2</td>
		</tr>
		<tr>
			<td>Stereomicroscope</td>
			<td>Zeiss&#160;</td>
			<td>495101-9804-000</td>
			<td>&#160;Stemi 2000 model. multiple brands manufacture similar items 
			http://microscopy.zeiss.com/microscopy/en_de/products/stereo-zoom-microscopes/stemi-2000.html</td>
		</tr>
		<tr>
			<td>Cold Light Source</td>
			<td>Zeiss</td>
			<td>000000-1063-182</td>
			<td>Multiple brands manufacture similar items 
			http://microscopy.zeiss.com/microscopy/en_de/products/microscope-components/lightsources.html</td>
		</tr>
		<tr>
			<td>Fluorescent Stereomicroscope&#160;</td>
			<td>Leica microsystems</td>
			<td>Contact Leica microsystems</td>
			<td>Leica M165-FC. Multiple brands manufacture similar items 
			http://www.leica-microsystems.com/products/stereo-microscopes-macroscopes/fluorescence/details/product/leica-m165-fc/</td>
		</tr>
		<tr>
			<td>Incubator Microscope +imaging software</td>
			<td>Olympus</td>
			<td>Contact Olympus</td>
			<td>Inverted microcope sealed inside a Co2 incubator. Vivaview FL incubator microscope with proprietry Metamorpoh imaging software. 
			http://olympuscanada.com/seg_section/product.asp?product=1055&#38;c=0</td>
		</tr>
		<tr>
			<td>Clean bench</td>
			<td>Thermo Scientific</td>
			<td>51029701</td>
			<td>Multiple brands manufacture similar items 
			http://www.thermoscientific.com/en/product/heraguard-eco-clean-bench.html</td>
		</tr>
		<tr>
			<td>CO2 incubator</td>
			<td>Thermo Scientific</td>
			<td>3310</td>
			<td>Multiple brands manufacture similar items 
			http://www.thermoscientific.com/en/products/co2-incubators.html</td>
		</tr>
		<tr>
			<td>Laminar Flow hood</td>
			<td>Thermo Scientific</td>
			<td>51026651</td>
			<td>Multiple brands manufacture similar items 
			http://www.thermoscientific.com/en/products/biological-safety-cabinets-clean-benches.html</td>
		</tr>
	</tbody>
</table>

long-term time lapse imaging of mouse cochlear explants

Here we present a method for long-term time-lapse imaging of live embryonic mouse cochlear explants. The developmental program responsible for building the highly ordered, complex structure of the mammalian cochlea proceeds for around ten days. In order to study changes in gene expression over this period and their response to pharmaceutical or genetic manipulation, long-term imaging is necessary. Previously, live imaging has typically been limited by the viability of explanted tissue in a humidified chamber atop a standard microscope. Difficulty in maintaining optimal conditions for culture growth with regard to humidity and temperature has placed limits on the length of imaging experiments. A microscope integrated into a modified tissue culture incubator provides an excellent environment for long term-live imaging. In this method we demonstrate how to establish embryonic mouse cochlear explants and how to use an incubator microscope to conduct time lapse imaging using both bright field and fluorescent microscopy to examine the behavior of a typical embryonic day (E) 13 cochlear explant and Sox2, a marker of the prosensory cells of the cochlea, over 5 days.

Here we show a montage (Figure 1) and a movie (Figure 2) demonstrating how a typical organotypic cochlear explant will grow if plated on E13.5. A Sox2 reporter mouse was used to visualize the prosensory region. The movie illustrates that the cochlea undergoes growth and convergence and extension, the cells in the lateral region of the green Sox2 domain do not seem to divide as the tissue surrounding it expands. This is a characteristic of the organ of Corti; on E13 the ...

Watch this Scientific Journal Video about Long-term Time Lapse Imaging of Mouse Cochlear Explants at JoVE.com

Long-term Time Lapse Imaging of Mouse Cochlear Explants

Live imaging of the embryonic mammalian cochlea is challenging because the developmental processes at hand operate on a temporal gradient over ten days. Here we present a method for culturing and then imaging embryonic cochlear explant tissue taken from a fluorescent reporter mouse over five days.

Here we present a method for long-term time-lapse imaging of live embryonic mouse cochlear explants. The developmental program responsible for building ...

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Neuroscience

9.5K Views.  Sunnybrook Research Institute. Live imaging of the embryonic mammalian cochlea is challenging because the developmental processes at hand operate on a temporal gradient over ten days. Here we present a method for culturing and then imaging embryonic cochlear explant tissue taken from a fluorescent reporter mouse over five days.

Video: Long-term Time Lapse Imaging of Mouse Cochlear Explants

Multiple-mouse Neuroanatomical Magnetic Resonance Imaging

The field of mouse phenotyping with magnetic resonance imaging (MRI) is rapidly growing, motivated by the need for improved tools for characterizing and evaluating mouse models of human disease. MRI is an excellent modality for investigating genetically altered animals. It is capable of whole brain coverage, can be used in vivo, and provides multiple contrast mechanisms for investigating different aspects of neuranatomy and physiology. The advent of high-field scanners along with the ability to scan multiple mice simultaneously allows for rapid phenotyping of novel mutations.
Effective mouse MRI studies require attention to many aspects of experiment design. In this article, we will describe general methods to acquire quality images for mouse phenotyping using a system that images mice concurrently in shielded transmit/receive radio frequency (RF) coils in a common magnet (Bock et al., 2003). We focus particularly on anatomical phenotyping, an important and accessible application that has shown a high potential for impact in many mouse models at our imaging centre. Before we can provide the detailed steps to acquire such images, there are important practical considerations for both in vivo brain imaging (Dazai et al., 2004) and ex vivo brain imaging (Spring et al., 2007) that should be noted. These are discussed below.

Magnetic resonance imaging (MRI) has become an increasingly popular tool for examining the phenotype of genetically altered mice. This article illustrates the methods necessary to achieve high-throughput phenotyping of genetically altered mice using multiple-mouse MRI.

The field of mouse phenotyping with magnetic resonance imaging (MRI) is rapidly growing, motivated by the need for improved tools for characterizing and ...

Time-lapse Live Imaging of Clonally Related Neural Progenitor Cells in the Developing Zebrafish Forebrain

Precise patterns of division, migration and differentiation of neural progenitor cells are crucial for proper brain development and function1,2. To understand the behavior of neural progenitor cells in the complex in vivo environment, time-lapse live imaging of neural progenitor cells in an intact brain is critically required. In this video, we exploit the unique features of zebrafish embryos to visualize the development of forebrain neural progenitor cells in vivo. We use electroporation to genetically and sparsely label individual neural progenitor cells. Briefly, DNA constructs coding for fluorescent markers were injected into the forebrain ventricle of 22 hours post fertilization (hpf) zebrafish embryos and electric pulses were delivered immediately. Six hours later, the electroporated zebrafish embryos were mounted with low melting point agarose in glass bottom culture dishes. Fluorescently labeled neural progenitor cells were then imaged for 36hours with fixed intervals under a confocal microscope using water dipping objective lens. The present method provides a way to gain insights into the in vivo development of forebrain neural progenitor cells and can be applied to other parts of the central nervous system of the zebrafish embryo.

The present video demonstrates a method which takes advantage of the combination of electroporation and confocal microscopy to perform live imaging on individual neural progenitor cells in the developing zebrafish forebrain. In vivo analysis of the development of forebrain neural progenitor cells at a clonal level can be achieved in this way.

Precise patterns of division, migration and differentiation of neural progenitor cells are crucial for proper brain development and function1,2. To ...

A Polished and Reinforced Thinned-skull Window for Long-term Imaging of the Mouse Brain

In vivo imaging of cortical function requires optical access to the brain without disruption of the intracranial environment. We present a method to form a polished and reinforced thinned skull (PoRTS) window in the mouse skull that spans several millimeters in diameter and is stable for months. The skull is thinned to 10 to 15 &mu;m in thickness with a hand held drill to achieve optical clarity, and is then overlaid with cyanoacrylate glue and a cover glass to: 1) provide rigidity, 2) inhibit bone regrowth and 3) reduce light scattering from irregularities on the bone surface. Since the skull is not breached, any inflammation that could affect the process being studied is greatly reduced. Imaging depths of up to 250 &mu;m below the cortical surface can be achieved using two-photon laser scanning microscopy. This window is well suited to study cerebral blood flow and cellular function in both anesthetized and awake preparations. It further offers the opportunity to manipulate cell activity using optogenetics or to disrupt blood flow in targeted vessels by irradiation of circulating photosensitizers.

We present a method to form an imaging window in the mouse skull that spans millimeters and is stable for months without inflammation of the brain. This method is well suited for longitudinal studies of blood flow, cellular dynamics, and cell/vascular structure using two-photon microscopy.

In vivo imaging of cortical function requires optical access to the brain without disruption of the intracranial environment. We present a method to form ...

Time-lapse Imaging of Neuroblast Migration in Acute Slices of the Adult Mouse Forebrain

There is a substantial body of evidence indicating that new functional neurons are constitutively generated from an endogenous pool of neural stem cells in restricted areas of the adult mammalian brain. Newborn neuroblasts from the subventricular zone (SVZ) migrate along the rostral migratory stream (RMS) to their final destination in the olfactory bulb (OB)1. In the RMS, neuroblasts migrate tangentially in chains ensheathed by astrocytic processes2,3 using blood vessels as a structural support and a source of molecular factors required for migration4,5. In the OB, neuroblasts detach from the chains and migrate radially into the different bulbar layers where they differentiate into interneurons and integrate into the existing network1, 6.
In this manuscript we describe the procedure for monitoring cell migration in acute slices of the rodent brain. The use of acute slices allows the assessment of cell migration in the microenvironment that closely resembling to in vivo conditions and in brain regions that are difficult to access for in vivo imaging. In addition, it avoids long culturing condition as in the case of organotypic and cell cultures that may eventually alter the migration properties of the cells. Neuronal precursors in acute slices can be visualized using DIC optics or fluorescent proteins. Viral labeling of neuronal precursors in the SVZ, grafting neuroblasts from reporter mice into the SVZ of wild-type mice, and using transgenic mice that express fluorescent protein in neuroblasts are all suitable methods for visualizing neuroblasts and following their migration. The later method, however, does not allow individual cells to be tracked for long periods of time because of the high density of labeled cells. We used a wide-field fluorescent upright microscope equipped with a CCD camera to achieve a relatively rapid acquisition interval (one image every 15 or 30 sec) to reliably identify the stationary and migratory phases. A precise identification of the duration of the stationary and migratory phases is crucial for the unambiguous interpretation of results. We also performed multiple z-step acquisitions to monitor neuroblasts migration in 3D. Wide-field fluorescent imaging has been used extensively to visualize neuronal migration7-10. Here, we describe detailed protocol for labeling neuroblasts, performing real-time video-imaging of neuroblast migration in acute slices of the adult mouse forebrain, and analyzing cell migration. While the described protocol exemplified the migration of neuroblasts in the adult RMS, it can also be used to follow cell migration in embryonic and early postnatal brains.

We describe a protocol for real-time videoimaging of neuronal migration in the mouse forebrain. The migration of virally-labeled or grafted neuronal precursors was recorded in acute live slices using wide-field fluorescent imaging with a relatively rapid acquisition interval to study the different phases of cell migration, including the durations of the stationary and migration phases and the speed of migration.

There is a substantial body of evidence indicating that new functional neurons are constitutively generated from an endogenous pool of neural stem cells ...

Motor Nerve Transection and Time-lapse Imaging of Glial Cell Behaviors in Live Zebrafish

The nervous system is often described as a hard-wired component of the body even though it is a considerably fluid organ system that reacts to external stimuli in a consistent, stereotyped manner, while maintaining incredible flexibility and plasticity. Unlike the central nervous system (CNS), the peripheral nervous system (PNS) is capable of significant repair, but we have only just begun to understand the cellular and molecular mechanisms that govern this phenomenon. Using zebrafish as a model system, we have the unprecedented opportunity to couple regenerative studies with in vivo imaging and genetic manipulation. Peripheral nerves are composed of axons surrounded by layers of glia and connective tissue. Axons are ensheathed by myelinating or non-myelinating Schwann cells, which are in turn wrapped into a fascicle by a cellular sheath called the perineurium. Following an injury, adult peripheral nerves have the remarkable capacity to remove damaged axonal debris and re-innervate targets. To investigate the roles of all peripheral glia in PNS regeneration, we describe here an axon transection assay that uses a commercially available nitrogen-pumped dye laser to axotomize motor nerves in live transgenic zebrafish. We further describe the methods to couple these experiments to time-lapse imaging of injured and control nerves. This experimental paradigm can be used to not only assess the role that glia play in nerve regeneration, but can also be the platform for elucidating the molecular mechanisms that govern nervous system repair.

Although the peripheral nervous system (PNS) is capable of significant repair after injury, little is known about the cellular and molecular mechanisms that govern this phenomenon. Using live, transgenic zebrafish and a reproducible nerve transection assay, we can study dynamic glial cell behaviors during nerve degeneration and regeneration.

The  nervous system is often described as a hard-wired component of the body even  though it is a considerably fluid organ system that reacts to external ...

In vivo Postnatal Electroporation and Time-lapse Imaging of Neuroblast Migration in Mouse Acute Brain Slices

The subventricular zone (SVZ) is one of the main neurogenic niches in the postnatal brain. Here, neural progenitors proliferate and give rise to neuroblasts able to move along the rostral migratory stream (RMS) towards the olfactory bulb (OB). This long-distance migration is required for the subsequent maturation of newborn neurons in the OB, but the molecular mechanisms regulating this process are still unclear. Investigating the signaling pathways controlling neuroblast motility may not only help understand a fundamental step in neurogenesis, but also have therapeutic regenerative potential, given the ability of these neuroblasts to target brain sites affected by injury, stroke, or degeneration.
In this manuscript we describe a detailed protocol for in vivo postnatal electroporation and subsequent time-lapse imaging of neuroblast migration in the mouse RMS. Postnatal electroporation can efficiently transfect SVZ progenitor cells, which in turn generate neuroblasts migrating along the RMS. Using confocal spinning disk time-lapse microscopy on acute brain slice cultures, neuroblast migration can be monitored in an environment closely resembling the in vivo condition. Moreover, neuroblast motility can be tracked and quantitatively analyzed. As an example, we describe how to use in vivo postnatal electroporation of a GFP-expressing plasmid to label and visualize neuroblasts migrating along the RMS. Electroporation of shRNA or CRE recombinase-expressing plasmids in conditional knockout mice employing the LoxP system can also be used to target genes of interest. Pharmacological manipulation of acute brain slice cultures can be performed to investigate the role of different signaling molecules in neuroblast migration. By coupling in vivo electroporation with time-lapse imaging, we hope to understand the molecular mechanisms controlling neuroblast motility and contribute to the development of novel approaches to promote brain repair.

In vivo Postnatal Electroporation and Time-lapse Imaging of Neuroblast Migration in Mouse Acute Brain Slices

Neuroblast migration is a fundamental event in postnatal neurogenesis. We describe a protocol for efficient labeling of neuroblasts by in vivo postnatal electroporation and subsequent visualization of their migration using time-lapse imaging of acute brain slices. We include a description for the quantitative analysis of neuroblast dynamics by video tracking.

The subventricular zone (SVZ) is one of the main neurogenic niches in the postnatal brain. Here, neural progenitors proliferate and give rise to ...

Agarose Microchambers for Long-term Calcium Imaging of Caenorhabditis elegans

Behavior is controlled by the nervous system. Calcium imaging is a straightforward method in the transparent nematode Caenorhabditis elegans to measure the activity of neurons during various behaviors. To correlate neural activity with behavior, the animal should not be immobilized but should be able to move. Many behavioral changes occur during long time scales and require recording over many hours of behavior. This also makes it necessary to culture the worms in the presence of food. How can worms be cultured and their neural activity imaged over long time scales? Agarose Microchamber Imaging (AMI) was previously developed to culture and observe small larvae and has now been adapted to study all life stages from early L1 until the adult stage of C. elegans. AMI can be performed on various life stages of C. elegans. Long-term calcium imaging is achieved without immobilizing the animals by using short externally triggered exposures combined with an electron multiplying charge-coupled device (EMCCD) camera recording. Zooming out or scanning can scale up this method to image up to 40 worms in parallel. Thus, a method is described to image behavior and neural activity over long time scales in all life stages of C. elegans.

Agarose Microchambers for Long-term Calcium Imaging of Caenorhabditis elegans

Imaging behavior and neural activity over long time scales without immobilization of the animal is a prerequisite to understand behavior. Agarose microfluidic chambers imaging (AMI) can be used to image neural activity and behavior for all life stages of Caenorhabditis elegans.

Behavior is controlled by the nervous system. Calcium imaging is a straightforward method in the transparent nematode Caenorhabditis elegans to measure ...

Time-lapse Confocal Imaging of Migrating Neurons in Organotypic Slice Culture of Embryonic Mouse Brain Using In Utero Electroporation

In utero electroporation is a rapid and powerful approach to study the process of radial migration in the cerebral cortex of developing mouse embryos. It has helped to describe the different steps of radial migration and characterize the molecular mechanisms controlling this process. To directly and dynamically analyze migrating neurons they have to be traced over time. This protocol describes a workflow that combines in utero electroporation with organotypic slice culture and time-lapse confocal imaging, which allows for a direct examination and dynamic analysis of radially migrating cortical neurons. Furthermore, detailed characterization of migrating neurons, such as migration speed, speed profiles, as well as radial orientation changes, is possible. The method can easily be adapted to perform functional analyses of genes of interest in radially migrating cortical neurons by loss and gain of function as well as rescue experiments. Time-lapse imaging of migrating neurons is a state-of-the-art technique that once established is a potent tool to study the development of the cerebral cortex in mouse models of neuronal migration disorders.

Time-lapse Confocal Imaging of Migrating Neurons in Organotypic Slice Culture of Embryonic Mouse Brain Using In Utero Electroporation

This protocol provides instructions for direct observation of radially migrating cortical neurons. In utero electroporation, organotypic slice culture, and time-lapse confocal imaging are combined to directly and dynamically study the effects of overexpression or downregulation of genes of interest in migrating neurons and to analyze their differentiation during development.

In utero electroporation is a rapid and powerful approach to study the process of radial migration in the cerebral cortex of developing mouse embryos. It ...

Time-lapse Live Imaging and Quantification of Fast Dendritic Branch Dynamics in Developing Drosophila Neurons

Highly motile dendritic filopodia are widely present in neurons at early developmental stages. These exploratory dynamic branches sample the surrounding environment and initiate contacts with potential synaptic partners. Although the connection between dendritic branch dynamics and synaptogenesis is well established, how developmental and activity-dependent processes regulate dendritic branch dynamics is not well understood. This is partly due to the technical difficulties associated with the live imaging and quantitative analyses of these fine structures using an in vivo system. We established a method to study dendrite dynamics using Drosophila larval ventral lateral neurons (LNvs), which can be individually labeled using genetic approaches and are accessible for live imaging. Taking advantage of this system, we developed protocols to capture branch dynamics of the whole dendritic arbor of a single labeled LNv through time-lapse live imaging. We then performed post-processing to improve image quality through drift correction and deconvolution, followed by analyzing branch dynamics at the single-branch level by annotating spatial positions of all branch terminals. Lastly, we developed R scripts (Supplementary File) and specific parameters to quantify branch dynamics using the coordinate information generated by the terminal tracing. Collectively, this protocol allows us to achieve a detailed quantitative description of branch dynamics of the neuronal dendritic arbor with high temporal and spatial resolution. The methods we developed are generally applicable to sparsely labeled neurons in both in vitro and in vivo conditions.

Time-lapse Live Imaging and Quantification of Fast Dendritic Branch Dynamics in Developing Drosophila Neurons

Here, we describe the method we employed to image highly motile dendritic filopodia in a live preparation of the Drosophila larval brain, and the protocol we developed to quantify time-lapse 3D imaging datasets for quantitative assessments of dendrite dynamics in developing neurons.

Highly motile dendritic filopodia are widely present in neurons at early developmental stages. These exploratory dynamic branches sample the surrounding ...

Long-Term, Serum-Free Cultivation of Organotypic Mouse Retina Explants with Intact Retinal Pigment Epithelium

In ophthalmic research, there is a strong need for in vitro models of the neuroretina. Here, we present a detailed protocol for organotypic culturing of the mouse neuroretina&#160;with intact retinal pigment epithelium (RPE). Depending on the research question, retinas can be isolated from wild-type animals or from disease models, to study, for instance, diabetic retinopathy or hereditary retinal degeneration. Eyes from early postnatal day 2&#8211;9 animals are enucleated under aseptic conditions. They are partially digested in proteinase K to allow for a detachment of the choroid from the RPE. Under the stereoscope, a small incision is made in the cornea creating two edges from where the choroid and sclera can be gently peeled off from the RPE and neuroretina. The lens is then removed, and the eyecup is cut in four points to give it a four-wedged shape resembling a clover leaf. The tissue is finally transferred in a hanging drop into a cell culture insert holding a polycarbonate culturing membrane. The cultures are then maintained in R16 medium, without serum or antibiotics, under entirely defined conditions, with a medium change every second day.
The procedure described enables the isolation of the retina and the preservation of its normal physiological and histotypic context for culturing periods of at least 2 weeks. These features make organotypic retinal explant cultures an excellent model with high predictive value, for studies into retinal development, disease mechanisms, and electrophysiology, while also enabling pharmacological screening.

The protocol describes organotypic explants of mouse neuroretina, cultivated together with its retinal pigment epithelium (RPE), in R16 defined medium, free of serum and antibiotics. This method is relatively simple to perform, less expensive, and time-consuming when compared to in vivo experiments, and can be adapted to numerous experimental applications.

In ophthalmic research, there is a strong need for in vitro models of the neuroretina. Here, we present a detailed protocol for organotypic culturing of ...