Research in the authors' laboratory is supported by the National Institutes of Health grants R37-HL041026, R01-HL086483 and R01-HL056786 (SSS) and by F32-HL097463 and T32-AR048523 (PB) from the United States Public Health Service.

1. Animal Care and Use
Following review and approval from the Institutional Animal Care and Use Committee, male mice at least 12 weeks old are used. A mouse is anesthetized with pentobarbital sodium (60 mg/kg) via intraperitoneal (i.p.) injection. Throughout surgical procedures and experimental protocols, anesthesia is maintained by supplements (10-20% of initial injection, i.p.) as needed (every 30-60 minutes; indicated by withdrawal response to toe or tail pinch). After completion of the experimental procedure the mouse is overdosed with pentobarbital (i.p.) and euthanized by cervical dislocation.
2. Micropipettes and Microiontophoresis
<ol>
 <li>Microiontophoresis micropipettes (internal tip diameter, &tilde;1 &mu;m) are prepared from borosilicate glass capillary tubes using a horizontal pipette puller. Ours 
 have a &tilde;5 mm taper for stiffness; longer tapers are more flexible.</li>
 <li>Micropipettes are backfilled with 1M ACh (Figure1A-C) dissolved in 18.2 M&Omega; water. For backfilling, a microcapillary tube is connected to 0.2 &mu;m filter coupled to a syringe containing the agonist of interest (Figure 1). These can be readily fabricated (below) or purchased from commercial vendors. The microcapillary tube is inserted into the back end of the micropipette and ACh solution is delivered into the lumen while withdrawing the microcapillary tube as the micropipette fills. Holding the micropipette with its tip pointing down, air bubbles are removed by gently flicking the micropipette.</li>
 <li>The micropipette is secured in a holder mounted in a micromanipulator (Figure 2). The holder has a silver wire connecting the ACh solution within the micropipette to an external pin, which in turn is connected to the positive terminal of a microiontophoresis programmer. A second silver wire secured at the edge of the tissue preparation is connected to the negative terminal to complete the circuit as the tip of the micropipette is advanced into the physiological saline solution over the preparation. </li>
 <li>A retaining current is applied to prevent vasodilation (or fluorescent response) when the micropipette tip is positioned adjacent to the arteriolar wall. Retaining current will vary with the size of the micropipette tip (internal diameter = 1 &mu;m) and agonist concentration but is highly reproducible for defined parameters (we use &tilde;200 nA for 1M ACh, 1 &mu;m tip). The retaining current ceases coincident with delivery of ejection current via the electronic trigger (Supplementary Figure 1) synchronized with the onset of image acquisition.</li>
</ol>
3. Micromanipulation
<ol>
 <li>A custom platform for an X-Y microscope stage was fabricated out of ferromagnetic stainless steel. Platform dimensions (1/8" X 12" X 13") enable sufficient space to position micromanipulators around the experimental preparation as desired (Figure 2A). Micromanipulators secured to magnetic bases (Figure 2B) enable positioning as dictated by the preparation. These are placed directly on the fabricated platform around the preparation for positioning micropipettes at sites of interest (Figure 2C). </li>
</ol>
4. Representative Results
<ol>
 <li>With the micropipette tip positioned adjacent to an arteriole, there is fluorescence response to ACh (retaining current than adjusted to prevent ACh leakage). Below a threshold stimulus there was no effect. However, as stimulus intensity increased, endothelial cell calcium fluorescence increased over progressively greater distances along the arteriole, as did the intensity of fluorescence at the site of stimulation (Figure 3).</li>
</ol>
<img src="/files/ftp_upload/2900/2900fig1.jpg" alt="Figure 1" /> 
Figure 1. Method for Backfilling Microiontophoresis Pipettes. A) A microcapillary tube (green arrow) is secured in a compression fitting (blue arrow) 
attached to a 0.2 &mu;m filter (purple arrow) which is then attached to a syringe filled with 1M ACh. B) The microcapillary tube is fed into the 
microiontophoresis pipette through the back end and solution is displaced to fill the lumen of the micropipette. C) Once the pipette is filled, hold the tip 
down and gently flick above the taper to remove bubbles (black arrow).
<img src="/files/ftp_upload/2900/2900fig2.jpg" alt="Figure 2" /> 
Figure 2. Custom Platform for Micromanipulator Placement. A) A ferromagnetic stainless steel platform was placed on a custom MVX10 microscope base 
containing an X-Y translational stage. B) Circular magnetic bases affixed to the bottom of compact 3-axis micromanipulators. C) 
Micromanipulators positioned around the experimental preparation (See associated protocol: JoVE ID#2874) to study specific sites of interest. Their 
compact size and versatility enable multiple micropipettes to be used simultaneously.
<img src="/files/ftp_upload/2900/2900fig3.jpg" alt="Figure 3" /> 
Figure 3. Calcium Fluorescence in Arterioles. Calcium fluorescence of endothelial cells lining the arteriolar wall increased with stimulus intensity. 
The first 3 panels shown images of fluorescence responses to A) 250 nA, B) 500 nA and C) 1000 nA ejection current (all 500 ms pulse duration). The distance over which 
endothelial cell calcium fluorescence increased is indicated by brackets in A-C (&tilde;130, 270 and 400 &mu;m, respectively). The reference line across the arteriole in each 
panel indicates where fluorescence responses (F/Fo) to ACh were recorded at the site of stimulation. D) Recordings of F/Fo vs. time for increasing ACh stimuli. As 
ejection current increased, F/Fo increased in amplitude and duration. Note that 100 nA stimulus was below threshold and had no effect. 
<img src="/files/ftp_upload/2900/2900sup1.jpg" alt="Supplementary Figure 1" /> 
Supplementary Figure 1. Circuit diagram for electronic trigger. This circuit is interfaced with a parallel port from a personal computer. When activated it provides a constant TTL pulse of 5V. The 7805 chip is a 5V voltage regulator connected to a 9-12V DC power supply (a battery of appropriate voltage is fine). Output from the 7805 provides power to the Quad Bilateral Switch and to the output of the circuit. Input across the 1K resistor is from the computer.

<ol>
	<li>Majno, G., Palade, G. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Studies+on+inflammation.+1.+The+effect+of+histamine+and+serotonin+on+vascular+permeability:+an+electron+microscopic+study.">Studies on inflammation. 1. The effect of histamine and serotonin on vascular permeability: an electron microscopic study.</a> J. Biophys. Biochem. Cytol. 11, 571-605 (1961).</li><li>Majno, G., Palade, G. E., Schoefl, G. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Studies+on+inflammation.+II.+The+site+of+action+of+histamine+and+serotonin+along+the+vascular+tree:+a+topographic+study.">Studies on inflammation. II. The site of action of histamine and serotonin along the vascular tree: a topographic study.</a> J. Biophys. Biochem. Cytol. 11, 607-626 (1961).</li><li>Grant, R. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+Observation+of+Skeletal+Muscle+Blood+Vessels+(Rat+Cremaster).">Direct Observation of Skeletal Muscle Blood Vessels (Rat Cremaster).</a> J. Physiol. 172, 123-137 (1964).</li><li>Baez, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+open+cremaster+muscle+preparation+for+the+study+of+blood+vessels+by+in+vivo+microscopy.">An open cremaster muscle preparation for the study of blood vessels by in vivo microscopy.</a> Microvasc. Res. 5, 384-394 (1973).</li><li>Bohlen, H. G., Gore, R. W., Hutchins, P. M. <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+microvascular+pressures+in+normal+and+spontaneously+hypertensive+rats.">Comparison of microvascular pressures in normal and spontaneously hypertensive rats.</a> Microvasc. Res. 13, 125-130 (1977).</li><li>Klitzman, B., Duling, B. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microvascular+hematocrit+and+red+cell+flow+in+resting+and+contracting+striated+muscle.">Microvascular hematocrit and red cell flow in resting and contracting striated muscle.</a> Am. J. Physiol. 237, 481-490 (1979).</li><li>Hungerford, J. E., Sessa, W. C., &amp;amp, S. e. g. a. l., S, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Vasomotor+control+in+arterioles+of+the+mouse+cremaster+muscle.">Vasomotor control in arterioles of the mouse cremaster muscle.</a> FASEB J. 14, 197-207 (2000).</li><li>Figueroa, X. F., Paul, D. L., Simon, A. M., Goodenough, D. A., Day, K. H., Damon, D. N., Duling, B. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Central+role+of+connexin40+in+the+propagation+of+electrically+activated+vasodilation+in+mouse+cremasteric+arterioles+in+vivo.">Central role of connexin40 in the propagation of electrically activated vasodilation in mouse cremasteric arterioles in vivo.</a> Circ. Res. 92, 793-800 (2003).</li><li>Wolfle, S. E., Schmidt, V. J., Hoepfl, B., Gebert, A., Alcolea, S., Gros, D., de Wit, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Connexin45+cannot+replace+the+function+of+connexin40+in+conducting+endothelium-dependent+dilations+along+arterioles.">Connexin45 cannot replace the function of connexin40 in conducting endothelium-dependent dilations along arterioles.</a> Circ. Res. 101, 292-1299 (2007).</li><li>Milkau, M., Kohler, R., de Wit, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Crucial+importance+of+the+endothelial+K++channel+SK3+and+connexin40+in+arteriolar+dilations+during+skeletal+muscle+contraction.">Crucial importance of the endothelial K+ channel SK3 and connexin40 in arteriolar dilations during skeletal muscle contraction.</a> FASEB J. 24, 3572-3579 (2010).</li><li>Bagher, P., Duan, D., Segal, S. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evidence+for+impaired+neurovascular+transmission+in+a+murine+model+of+Duchenne+Muscular+Dystrophy.">Evidence for impaired neurovascular transmission in a murine model of Duchenne Muscular Dystrophy.</a> J. Appl. Physiol. 110, 601-610 (2011).</li><li>Tallini, Y. N., Brekke, J. F., Shui, B., Doran, R., Hwang, S. M., Nakai, J., Salama, G., Segal, S. S., Kotlikoff, M. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Propagated+endothelial+Ca2++waves+and+arteriolar+dilation+in+vivo:+measurements+in+Cx40BAC-GCaMP2+transgenic+mice.">Propagated endothelial Ca2+ waves and arteriolar dilation in vivo: measurements in Cx40BAC-GCaMP2 transgenic mice.</a> Circ. Res. 101, 1300-1309 (2007).</li><li>Grant, R. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+effects+of+denervation+on+skeletal+muscle+blood+vessels+(rat+cremaster).">The effects of denervation on skeletal muscle blood vessels (rat cremaster).</a> J. Anat. 100, 305-316 (1966).</li><li>Proctor, K. G., Busija, D. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Relationships+among+arteriolar,+regional,+and+whole+organ+blood+flow+in+cremaster+muscle.">Relationships among arteriolar, regional, and whole organ blood flow in cremaster muscle.</a> Am. J. Physiol. 249, H34-H41 (1985).</li><li>Bagher, P., Segal, S. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+blood+flow+in+the+microcirculation:+Role+of+conducted+vasodilation.">Regulation of blood flow in the microcirculation: Role of conducted vasodilation.</a> Acta Physiol. , (2011).</li><li>Hill, M. A., Simpson, B. E., Meininger, G. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Altered+cremaster+muscle+hemodynamics+due+to+disruption+of+the+deferential+feed+vessels.">Altered cremaster muscle hemodynamics due to disruption of the deferential feed vessels.</a> Microvasc. Res. 39, 349-363 (1990).</li></ol>

All procedures and protocols involving animals were approved by the Animal Care and Use Committee of the University of Missouri and performed in accord with the National Institutes of Health Guide for the Care and Use of Laboratory Animals. Production of this article was sponsored by Stanford Photonics.

The protocol described here demonstrates methods for preparing and implementing micropipettes for microiontophoresis. Delivery of acetylcholine is used to illustrate calcium signaling underlying endothelium-dependent vasodilation in arterioles of the anesthetized mouse. Our results illustrate that the distance over which ACh increases endothelial cell calcium fluorescence increases with the intensity of ejection current from the microiontophoresis micropipette (Figure 3). The lack of fluorescence increase under resting conditions indicates negligible leakage of ACh from the micropipette. The lack of response to 100 nA stimulus intensity (Figure 3, legend) illustrates that a threshold intensity of stimulation is required for endothelial cell calcium to increase. These techniques can be readily adapted to other vasoactive agents and tissue preparations. 
Practical considerations: In working with microiontophoresis to study arteriolar reactivity, several things should be recognized. While it has proven difficult to determine the actual concentration of agonist delivered, stimulus-response curves are reproducible within and between preparations. These can be performed by holding pulse duration constant (e.g., 500 ms) and varying the ejection current (e.g., 250, 500 and 1000 nA; Figure 3). Alternatively, ejection current can be held constant (e.g., 500 nA) and pulse duration varied (e.g., 250, 500 and 1000 ms). For a reference to the actions of a defined agonist concentration, the preparation can be superfused with the appropriate solution5. Because the driving force for solute ejection is electrical charge movement, the agent to be delivered must carry a net charge to be displaced from the micropipette. To ensure that the agent of interest is the primary charge carrier, it is dissolved at high concentration (e.g., 1 M for ACh) to minimize electro-osmosis. When this requires manipulating the pH of the micropipette filling solution, vehicle controls are required to ascertain any nonspecific effects. Appropriate controls should also be performed for the passage of current alone (e.g., using micropipettes filled with isotonic saline). The effective distance for diffusion of the agent from its site of release should be ascertained and is most readily determined empirically by the disappearance of a physiological response (e.g., vasodilation or a rise in intracellular calcium upon ejection of ACh) as the micropipette is positioned at defined distances from the target site. In practice, the effective diffusion distance is greatly influenced by how the tip of the micropipette is positioned in the tissue; e.g. if the tip pressed down into the tissue and its tip is occluded, than ejection is impaired. Excessive connective tissue is particularly troublesome and should be removed from the tissue surface during surgical preparation. Attention should also be given to the possibility of depleting the tip of the designated agent. This is minimized by using relatively short pulses (e.g., &le; 1 s). With sustained currents (e.g., several seconds), the agonist may be expelled from the tip more rapidly than it can be replaced by diffusion from the bulk filling solution in the micropipette.
Because negligible volume is displaced with microiontophoresis, if one is trying to change the local ionic milieu (e.g., to deliver a depolarizing K+ stimulus), this cannot be effectively accomplished with microiontophoresis but is readily achieved with pressure ejection of bulk fluid having the desired composition. For local stimulation of an arteriole, micropipette tips with internal diameters of 2-3 &mu;m work well with ejection pressure 4-5 psi (28-35 kPa) and pulse duration (e.g., 1 second) controlled with a solenoid valve10. Where sustained delivery of an agent from a micropipette onto a microvessel is required, pressure ejection is preferred using micropipettes of appropriate internal tip diameter (e.g., &tilde;10 &mu;m)11,12. A hydrostatic column of known height with a stopcock valve provides an inexpensive, well-defined on/off constant pressure head. Flow rates are determined by the inner diameter of the pipette tip and the driving pressure. As always, vehicle controls are essential to exclude nonspecific actions of pressure ejection.

<table>
	<tbody>
		<tr>
			<td>Material Used</td>
			<td>Company</td>
			<td>Catalogue number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Borosilicate Glass Capillary Tubes</td>
			<td>Warner Instruments</td>
			<td>GC120F-10</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Horizontal Pipette Puller</td>
			<td>Sutter Instruments</td>
			<td>model P-97</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Acetylcholine Chloride</td>
			<td>Sigma-Aldrich</td>
			<td>A6625</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>adapter for Luer hub</td>
			<td>Martech</td>
			<td>AC1343</td>
			<td>To secure microcapillary tubing</td>
		</tr>
		<tr>
			<td>0.2 &mu;m Nylon Titan filter</td>
			<td>Sun Sri</td>
			<td>42204-NN</td>
			<td>Low retention volume to minimize loss</td>
		</tr>
		<tr>
			<td>5 ml syringe</td>
			<td>Becton-Dickinson Co.</td>
			<td>309603</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Pipette Holder</td>
			<td>Warner Instruments</td>
			<td>E45W-M12VH</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Silver Wire</td>
			<td>Warner Instruments</td>
			<td>AG10W</td>
			<td>0.25mm diameter</td>
		</tr>
		<tr>
			<td>3-axis micromanipulator</td>
			<td>Siskiyou Design Instruments</td>
			<td>DT3-100, MXB, MXC, MGB/8</td>
			<td>Components for manipulator as shown</td>
		</tr>
		<tr>
			<td>microiontophoresis current programmer</td>
			<td>World Precision Instruments</td>
			<td>Model 260</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>trigger device</td>
			<td>Custom</td>
			<td>custom</td>
			<td>circuit provided in Suppl. Figure 1</td>
		</tr>
		<tr>
			<td>stainless steel plate</td>
			<td>McMaster-Carr</td>
			<td>1/8" X 12" X 12" </td>
			<td>According to design</td>
		</tr>
		<tr>
			<td>Intensified Digital Camera</td>
			<td>Stanford Photonics Inc</td>
			<td>XR/Mega-10</td>
			<td>Integrated with Piper Control software</td>
		</tr>
	</tbody>
</table>

microiontophoresis and micromanipulation for intravital fluorescence imaging of the microcirculation

Microiontophoresis entails passage of current through a micropipette tip to deliver a solute at a designated site within an experimental preparation. Microiontophoresis can simulate synaptic transmission1 by delivering neurotransmitters and neuropeptides onto neurons reproducibly2. Negligible volume (fluid) displacement avoids mechanical disturbance to the experimental preparation. Adapting these techniques to the microcirculation3 has enabled mechanisms of vasodilation and vasoconstriction to be studied at the microscopic level in vivo4,5. A key advantage of such localized delivery is enabling vasomotor responses to be studied at defined sites within a microvascular network without evoking systemic or reflexive changes in blood pressure and tissue blood flow, thereby revealing intrinsic properties of microvessels.
A limitation of microiontophoresis is that the precise concentration of agent delivered to the site of interest is difficult to ascertain6. Nevertheless, its release from the micropipette tip is proportional to the intensity and duration of the ejection current2,7, such that reproducible stimulus-response relationships can be readily determined under defined experimental conditions (described below). Additional factors affecting microiontophoretic delivery include solute concentration and its ionization in solution. The internal diameter of the micropipette tip should be &tilde; 1 &mu;m or less to minimize diffusional 'leak', which can be counteracted with a retaining current. Thus an outward (positive) current is used to eject a cation and a negative current used to retain it within the micropipette.
Fabrication of micropipettes is facilitated with sophisticated electronic pullers8. Micropipettes are pulled from glass capillary tubes containing a filament that 'wicks' solution into the tip of the micropipette when filled from the back end ("backfilled"). This is done by inserting a microcapillary tube connected to a syringe containing the solution of interest and ejecting the solution into the lumen of the micropipette. Micromanipulators enable desired placement of micropipettes within the experimental preparation. Micromanipulators mounted on a movable base can be positioned around the preparation according to the topography of microvascular networks (developed below). 
The present protocol demonstrates microiontophoresis of acetylcholine (ACh+ Cl-) onto an arteriole of the mouse cremaster muscle preparation (See associated protocol: JoVE ID#2874) to produce endothelium-dependent vasodilation. Stimulus delivery is synchronized with digitized image acquisition using an electronic trigger. The use of Cx40BAC-GCaMP2 transgenic mice9 enables visualization of intracellular calcium responses underlying vasodilation in arteriolar endothelial cells in the living microcirculation.

Watch this Scientific Journal Video about Microiontophoresis and Micromanipulation for Intravital Fluorescence Imaging of the Microcirculation at JoVE.com

Microiontophoresis and Micromanipulation for Intravital Fluorescence Imaging of the Microcirculation

Microiontophoresis entails movement of ions from a micropipette in response to a difference in electrical potential between the inside and outside of the micropipette. Biologically active molecules are thereby delivered in proportion to electrical current. We illustrate acetylcholine microiontophoresis in conjunction with micromanipulation to study endothelium-dependent vasodilation in the microcirculation.

Microiontophoresis entails passage of current through a micropipette tip to deliver a solute at a designated site within an experimental  preparation. ...

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14.3K Views.  University of Missouri. Microiontophoresis entails movement of ions from a micropipette in response to a difference in electrical potential between the inside and outside of the micropipette. Biologically active molecules are thereby delivered in proportion to electrical current. We illustrate acetylcholine microiontophoresis in conjunction with micromanipulation to study endothelium-dependent vasodilation in the microcirculation.

Video: Microiontophoresis and Micromanipulation for Intravital Fluorescence Imaging of the Microcirculation

Born Normalization for Fluorescence Optical Projection Tomography for Whole Heart Imaging

Optical projection tomography is a three-dimensional imaging technique that has been recently introduced as an imaging tool primarily in developmental biology and gene expression studies. The technique renders biological sample optically transparent by first dehydrating them and then placing in a mixture of benzyl alcohol and benzyl benzoate in a 2:1 ratio (BABB or Murray s Clear solution). The technique renders biological samples optically transparent by first dehydrating them in graded ethanol solutions then placing them in a mixture of benzyl alcohol and benzyl benzoate in a 2:1 ratio (BABB or Murray s Clear solution) to clear. After the clearing process the scattering contribution in the sample can be greatly reduced and made almost negligible while the absorption contribution cannot be eliminated completely. When trying to reconstruct the fluorescence distribution within the sample under investigation, this contribution affects the reconstructions and leads, inevitably, to image artifacts and quantification errors.. While absorption could be reduced further with a permanence of weeks or months in the clearing media, this will lead to progressive loss of fluorescence and to an unrealistically long sample processing time. This is true when reconstructing both exogenous contrast agents (molecular contrast agents) as well as endogenous contrast (e.g. reconstructions of genetically expressed fluorescent proteins).

We suggest a Born normalized approach for Optical Projection Tomography (BnOPT) that accounts for the absorption properties of imaged samples to obtain accurate and quantitative fluorescence tomographic reconstructions. We use the proposed algorithm to reconstruct the fluorescence molecular probe distribution within small animal organs.

Optical projection tomography is a three-dimensional imaging technique that has been recently introduced as an imaging tool primarily in developmental ...

Mesoscopic Fluorescence Tomography for In-vivo Imaging of Developing Drosophila

Visualizing developing organ formation as well as progession and treatment of disease often heavily relies on the ability to optically interrogate molecular and functional changes in intact living organisms. Most existing optical imaging methods are inadequate for imaging at dimensions that lie between the penetration limits of modern optical microscopy (0.5-1mm) and the diffusion-imposed limits of optical macroscopy (&gt;1cm) [1]. Thus, many important model organisms, e.g. insects, animal embryos or small animal extremities, remain inaccessible for in-vivo optical imaging. 
Although there is increasing interest towards the development of nanometer-resolution optical imaging methods, there have not been many successful efforts in improving the imaging penetration depth. The ability to perform in-vivo imaging beyond microscopy limits is in fact met with the difficulties associated with photon scattering present in tissues. Recent efforts to image entire embryos for example [2,3] require special chemical treatment of the specimen, to clear them from scattering, a procedure that makes them suitable only for post-mortem imaging. These methods however evidence the need for imaging larger specimens than the ones usually allowed by two-photon or confocal microscopy, especially in developmental biology and in drug discovery.
We have developed a new optical imaging technique named Mesoscopic Fluorescence Tomography [4], which appropriate for non-invasive in-vivo imaging at dimensions of 1mm-5mm. The method exchanges resolution for penetration depth, but offers unprecedented tomographic imaging performance and it has been developed to add time as a new dimension in developmental biology observations (and possibly other areas of biological research) by imparting the ability to image the evolution of fluorescence-tagged responses over time. As such it can accelerate studies of morphological or functional dependencies on gene mutations or external stimuli, and can importantly, capture the complete picture of development or tissue function by allowing longitudinal time-lapse visualization of the same, developing organism.
The technique utilizes a modified laboratory microscope and multi-projection illumination to collect data at 360-degree projections. It applies the Fermi simplification to Fokker-Plank solution of the photon transport equation, combined with geometrical optics principles in order to build a realistic inversion scheme suitable for mesoscopic range. This allows in-vivo whole-body visualization of non-transparent three-dimensional structures in samples up to several millimeters in size.
We have demonstrated the in-vivo performance of the technique by imaging three-dimensional structures of developing Drosophila tissues in-vivo and by following the morphogenesis of the wings in the opaque Drosophila pupae in real time over six consecutive hours.

Mesoscopic Fluorescence Tomography for In-vivo Imaging of Developing Drosophila

Mesoscopic fluorescence tomography operates beyond the penetration limits of tissue-sectioning fluorescence microscopy. The technique is based on multi-projection illumination and a photon transport description. We demonstrate in-vivo whole-body 3D visualization of the morphogenesis of GFP-expressing wing imaginal discs in Drosophila melanogaster.

Visualizing  developing organ formation as well as progession and treatment of disease often  heavily relies on the ability to optically interrogate ...

Time-lapse Imaging of Mitosis After siRNA Transfection

Changes in cellular organization and chromosome dynamics that occur during mitosis are tightly coordinated to ensure accurate inheritance of genomic and cellular content. Hallmark events of mitosis, such as chromosome movement, can be readily tracked on an individual cell basis using time-lapse fluorescence microscopy of mammalian cell lines expressing specific GFP-tagged proteins. In combination with RNAi-based depletion, this can be a powerful method for pinpointing the stage(s) of mitosis where defects occur after levels of a particular protein have been lowered. In this protocol, we present a basic method for assessing the effect of depleting a potential mitotic regulatory protein on the timing of mitosis. Cells are transfected with siRNA, placed in a stage-top incubation chamber, and imaged using an automated fluorescence microscope. We describe how to use software to set up a time-lapse experiment, how to process the image sequences to make either still-image montages or movies, and how to quantify and analyze the timing of mitotic stages using a cell-line expressing mCherry-tagged histone H2B. Finally, we discuss important considerations for designing a time-lapse experiment. This strategy is complementary to other approaches and offers the advantages of 1) sensitivity to changes in kinetics that might not be observed when looking at cells as a population and 2) analysis of mitosis without the need to synchronize the cell cycle using drug treatments. The visual information from such imaging experiments not only allows the sub-stages of mitosis to be assessed, but can also provide unexpected insight that would not be apparent from cell cycle analysis by FACS.

Here we describe a basic protocol to image and quantify the mitotic timing of live mammalian tissue culture cells after siRNA transfection.

Changes in cellular organization and chromosome dynamics that occur during mitosis are tightly coordinated to ensure accurate inheritance of genomic and ...

The Mouse Cremaster Muscle Preparation for Intravital Imaging of the Microcirculation

Throughout the body, the maintenance of homeostasis requires the constant supply of oxygen and nutrients concomitant with removal of metabolic by-products. This balance is achieved by the movement of blood through the microcirculation, which encompasses the smallest branches of the vascular supply throughout all tissues and organs. Arterioles branch from arteries to form networks that control the distribution and magnitude of oxygenated blood flowing into the multitude of capillaries intimately associated with parenchymal cells. Capillaries provide a large surface area for diffusional exchange between tissue cells and the blood supply. Venules collect capillary effluent and converge as they return deoxygenated blood towards the heart. To observe these processes in real time requires an experimental approach for visualizing and manipulating the living microcirculation.
The cremaster muscle of rats was first used as a model for studying inflammation using histology and electron microscopy post mortem1,2. 
The first in vivo report of the exposed intact rat cremaster muscle investigated microvascular responses to vasoactive drugs using reflected light3. However 
curvature of the muscle and lack of focused illumination limited the usefulness of this preparation. The major breakthrough entailed opening the muscle, 
detaching it from the testicle and spreading it radially as a flat sheet for transillumination under a compound microscope4. While shown to be a valuable 
preparation to study the physiology of the microcirculation in rats5 and hamsters6, the cremaster muscle in mice7 has proven particularly useful in dissecting 
cellular pathways involved in regulating microvascular function8-11 and real-time imaging of intercellular signaling12. 
The cremaster muscle is derived from the internal oblique and transverse abdominus muscles as the testes descend through the inguinal canal13. 
It serves to support (Greek: cremaster = suspender) and maintain temperature of the testes. As described here, the cremaster muscle is prepared as a thin flat sheet 
for outstanding optical resolution. With the mouse maintained at a stable body temperature and plane of anesthesia, surgical preparation involves freeing the muscle 
from surrounding tissue and the testes, spreading it onto transparent pedestal of silastic rubber and securing the edges with insect pins while irrigating it 
continuously with physiological salt solution. The present protocol utilizes transgenic mice expressing GCaMP2 in arteriolar endothelial cells. GCaMP2 is a 
genetically encoded fluorescent calcium indicator molecule12. Widefield imaging and an intensified charge-coupled device camera enable in vivo study of 
calcium signaling in the arteriolar endothelium.

A tissue preparation is described for visualization and experimental manipulation of the living microcirculation. In anesthetized male mice, the thin, highly vascularized cremaster muscle is prepared for intravital microscopy to study microvascular networks including arterioles, capillaries and venules. This preparation is readily adapted for rats and hamsters.

Throughout the body, the maintenance of homeostasis requires the constant supply of oxygen and nutrients concomitant with removal of metabolic ...

Intravital Microscopy of the Microcirculation in the Mouse Cremaster Muscle for the Analysis of Peripheral Stem Cell Migration

In the era of intravascular cell application protocols in the context of regenerative cell therapy, the underlying mechanisms of stem cell migration to nonmarrow tissue have not been completely clarified. We describe here the technique of intravital microscopy applied to the mouse cremaster microcirculation for analysis of peripheral bone marrow stem cell migration in vivo. Intravital microscopy of the M. cremaster has been previously introduced in the field of inflammatory research for direct observation of leucocyte interaction with the vascular endothelium. Since sufficient peripheral stem and progenitor cell migration includes similar initial steps of rolling along and firm adhesion at the endothelial lining it is conceivable to apply the M. cremaster model for the observation and quantification of the interaction of intravasculary administered stem cells with the endothelium. As various chemical components can be selectively applied to the target tissue by simple superfusion techniques, it is possible to establish essential microenvironmental preconditions, for initial stem cell recruitment to take place in a living organism outside the bone marrow.

Intravital microscopy of the mouse M. cremaster microcirculation offers a unique and well-standardized in vivo model for the analysis of peripheral bone marrow stem cell migration.

In the era of intravascular cell application protocols in the context of regenerative cell therapy, the underlying mechanisms of stem cell migration to ...

Intravital Microscopy for Imaging Subcellular Structures in Live Mice Expressing Fluorescent Proteins

Here we describe a procedure to image subcellular structures in live rodents that is based on the use of confocal intravital microscopy. As a model organ, we use the salivary glands of live mice since they provide several advantages. First, they can be easily exposed to enable access to the optics, and stabilized to facilitate the reduction of the motion artifacts due to heartbeat and respiration. This significantly facilitates imaging and tracking small subcellular structures. Second, most of the cell populations of the salivary glands are accessible from the surface of the organ. This permits the use of confocal microscopy that has a higher spatial resolution than other techniques that have been used for in vivo imaging, such as two-photon microscopy. Finally, salivary glands can be easily manipulated pharmacologically and genetically, thus providing a robust system to investigate biological processes at a molecular level.
In this study we focus on a protocol designed to follow the kinetics of the exocytosis of secretory granules in acinar cells and the dynamics of the apical plasma membrane where the secretory granules fuse upon stimulation of the beta-adrenergic receptors. Specifically, we used a transgenic mouse that co-expresses cytosolic GFP and a membrane-targeted peptide fused with the fluorescent protein tandem-Tomato. However, the procedures that we used to stabilize and image the salivary glands can be extended to other mouse models and coupled to other approaches to label in vivo cellular components, enabling the visualization of various subcellular structures, such as endosomes, lysosomes, mitochondria, and the actin cytoskeleton.

Intravital microscopy is a powerful tool that enables imaging various biological processes in live animals. In this article, we present a detailed method for imaging the dynamics of subcellular structures, such as the secretory granules, in the salivary glands of live mice.

Here we describe a procedure to image subcellular structures in live rodents that is based on the use of confocal intravital microscopy. As a model organ, ...

Rapid Analysis and Exploration of Fluorescence Microscopy Images

Despite rapid advances in high-throughput microscopy, quantitative image-based assays still pose significant challenges. While a variety of specialized image analysis tools are available, most traditional image-analysis-based workflows have steep learning curves (for fine tuning of analysis parameters) and result in long turnaround times between imaging and analysis. In particular, cell segmentation, the process of identifying individual cells in an image, is a major bottleneck in this regard.
Here we present an alternate, cell-segmentation-free workflow based on PhenoRipper, an open-source software platform designed for the rapid analysis and exploration of microscopy images. The pipeline presented here is optimized for immunofluorescence microscopy images of cell cultures and requires minimal user intervention. Within half an hour, PhenoRipper can analyze data from a typical 96-well experiment and generate image profiles. Users can then visually explore their data, perform quality control on their experiment, ensure response to perturbations and check reproducibility of replicates. This facilitates a rapid feedback cycle between analysis and experiment, which is crucial during assay optimization. This protocol is useful not just as a first pass analysis for quality control, but also may be used as an end-to-end solution, especially for screening. The workflow described here scales to large data sets such as those generated by high-throughput screens, and has been shown to group experimental conditions by phenotype accurately over a wide range of biological systems. The PhenoBrowser interface provides an intuitive framework to explore the phenotypic space and relate image properties to biological annotations. Taken together, the protocol described here will lower the barriers to adopting quantitative analysis of image based screens.

Here we describe a workflow for rapidly analyzing and exploring collections of fluorescence microscopy images using PhenoRipper, a recently developed image-analysis platform.

Despite rapid advances in high-throughput microscopy, quantitative image-based assays still pose significant challenges. While a variety of specialized ...

Fluorescence Imaging with One-nanometer Accuracy (FIONA)

Fluorescence imaging with one-nanometer accuracy (FIONA) is a simple but useful technique for localizing single fluorophores with nanometer precision in the x-y plane. Here a summary of the FIONA technique is reported and examples of research that have been performed using FIONA are briefly described. First, how to set up the required equipment for FIONA experiments, i.e., a total internal reflection fluorescence microscopy (TIRFM), with details on aligning the optics, is described. Then how to carry out a simple FIONA experiment on localizing immobilized Cy3-DNA single molecules using appropriate protocols, followed by the use of FIONA to measure the 36 nm step size of a single truncated myosin Va motor labeled with a quantum dot, is illustrated. Lastly, recent effort to extend the application of FIONA to thick samples is reported. It is shown that, using a water immersion objective and quantum dots soaked deep in sol-gels and rabbit eye corneas (&#62;200 &#181;m), localization precision of 2-3 nm can be achieved.

Fluorescence Imaging with One-nanometer Accuracy FIONA

Single fluorophores can be localized with nanometer precision using FIONA. Here a summary of the FIONA technique is reported, and how to carry out FIONA experiments is described.

Fluorescence imaging with one-nanometer accuracy (FIONA) is a simple but useful technique for localizing single fluorophores with nanometer precision in ...

Micromanipulation Techniques Allowing Analysis of Morphogenetic Dynamics and Turnover of Cytoskeletal Regulators

Examining the spatiotemporal dynamics of proteins can reveal their functional importance in various contexts. In this article, it is discussed how fluorescent recovery after photobleaching (FRAP) and photoactivation techniques can be used to study the spatiotemporal dynamics of proteins in subcellular locations. We also show how these techniques enable straightforward determination of various parameters linked to actin cytoskeletal regulation and cell motility. Moreover, the microinjection of cells is additionally described as an alternative treatment (potentially preceding or complementing the aforementioned photomanipulation techniques) to trigger instantaneous effects of translocated proteins on cell morphology and function. Micromanipulation such as protein injection or local application of plasma membrane-permeable drugs or cytoskeletal inhibitors can serve as powerful tool to record immediate consequences of a given treatment on cell behavior at the single cell and subcellular level. This is exemplified here by immediate induction of lamellipodial cell edge protrusion by the injection of recombinant Rac1 protein, as established a quarter-century ago. In addition, we provide a protocol for determining the turnover of enhanced green fluorescent protein (EGFP)-VASP, an actin filament polymerase prominently accumulating at lamellipodial tips of B16-F1 cells, employing FRAP and including associated data analysis and curve fitting. We also present guidelines for estimating the rates of lamellipodial actin network polymerization, as exemplified by cells expressing EGFP-tagged &#946;-actin. Finally, instructions are given for how to investigate the rates of actin monomer mobility within the cell cytoplasm, followed by actin incorporation at sites of rapid filament assembly, such as the tips of protruding lamellipodia, using photoactivation approaches. None of these protocols is&#160;restricted to components or regulators of the actin cytoskeleton, but can easily be extended to explore in analogous fashion the spatiotemporal dynamics and function of proteins in various different subcellular structures or functional contexts.

We describe how micro- and photomanipulation techniques such as FRAP and photoactivation enable the determination of motility parameters and the spatiotemporal dynamics of proteins within migrating cells. Experimental readouts include subcellular dynamics and turnover of motility regulators or of the underlying actin cytoskeleton.

Examining the spatiotemporal dynamics of proteins can reveal their functional importance in various contexts. In this article, it is discussed how ...

Isolation and Fluorescence Imaging for Single-particle Reconstruction of Chlamydomonas Centrioles

Centrioles are large macromolecular assemblies important for the proper execution of fundamental cell biological processes such as cell division, cell motility, or cell signaling. The green algae Chlamydomonas reinhardtii has proven to be an insightful model in the study of centriole architecture, function, and protein composition. Despite great advances toward understanding centriolar architecture, one of the current challenges is to determine the precise localization of centriolar components within structural regions of the centriole in order to better understand their role in centriole biogenesis. A major limitation lies in the resolution of fluorescence microscopy, which complicates the interpretation of protein localization in this organelle with dimensions close to the diffraction limit. To tackle this question, we are providing a method to purify and image a large number of C. reinhardtii centrioles with different orientations using super-resolution microscopy. This technique allows further processing of data through fluorescent single-particle averaging (Fluo-SPA) owing to the large number of centrioles acquired. Fluo-SPA generates averages of stained C. reinhardtii centrioles in different orientations, thus facilitating the localization of distinct proteins in centriolar sub-regions. Importantly, this method can be applied to image centrioles from other species or other large macromolecular assemblies.

Isolation and Fluorescence Imaging for Single-particle Reconstruction of Chlamydomonas Centrioles

We have developed a strategy to purify and image a large number of centrioles in different orientations amenable for super-resolution microscopy and single-particle averaging.

Centrioles are large macromolecular assemblies important for the proper execution of fundamental cell biological processes such as cell division, cell ...