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        <title>Sample Imaging — CLARITY forum</title>
        <link>https://forum.claritytechniques.org/</link>
        <pubDate>Sat, 08 Aug 2026 00:22:04 +0000</pubDate>
        <language>en</language>
            <description>Sample Imaging — CLARITY forum</description>
    <atom:link href="https://forum.claritytechniques.org/categories/sample-imaging/feed.rss" rel="self" type="application/rss+xml"/>
    <item>
        <title>Sample moving under scope</title>
        <link>https://forum.claritytechniques.org/discussion/196/sample-moving-under-scope</link>
        <pubDate>Fri, 31 Mar 2017 18:02:26 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>cmcabral</dc:creator>
        <guid isPermaLink="false">196@/discussions</guid>
        <description><![CDATA[Hello everyone,

I seem to be having a problem with imaging at high magnification.  I need to image at 60X to evaluate spine densities but even at 40X, the objective seems to need to be so close to the coverslip that there is pressure which causes the sample to float away in the mounting media.  Has anyone else had this issue?  I would appreciate any suggestions/advice.  I am only trying to image through a 200um thick section so this should not be a problem at all yet here we are.]]>
        </description>
    </item>
    <item>
        <title>Mounting for imaging</title>
        <link>https://forum.claritytechniques.org/discussion/50/mounting-for-imaging</link>
        <pubDate>Tue, 13 Aug 2013 22:44:59 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>Jalal</dc:creator>
        <guid isPermaLink="false">50@/discussions</guid>
        <description><![CDATA[After incubating in focus clear, the protocol says to mount in a chamber covered with a Wllco dish.  Has anyone tried using simple coverslips?  

We have Corning 1 1/2 cover slips that are about the same thickness of the glass bottoms of the Willco dish (~.17mm).  May give them a try, but maybe the refractive properties are different.  

If anyone has come up with a fun mounting solution that works, I'd be happy to hear it!]]>
        </description>
    </item>
    <item>
        <title>ScaleS autofluorescence</title>
        <link>https://forum.claritytechniques.org/discussion/195/scales-autofluorescence</link>
        <pubDate>Tue, 28 Mar 2017 02:43:46 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>ms91136</dc:creator>
        <guid isPermaLink="false">195@/discussions</guid>
        <description><![CDATA[Has anyone tried ScaleS to clear mouse brains? I had trouble imaging due to brain tissues auto-fluorescing.  ]]>
        </description>
    </item>
    <item>
        <title>FocusClear</title>
        <link>https://forum.claritytechniques.org/discussion/1/focusclear</link>
        <pubDate>Tue, 18 Jun 2013 04:51:32 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>nicolasrenier</dc:creator>
        <guid isPermaLink="false">1@/discussions</guid>
        <description><![CDATA[It seems that using the FocusClear(r) reagent is paramount to obtain the best transparency. However, this mounting medium is expensive, and seems to be back-ordered for a while due to large demand. Also, the formulation is proprietary, which makes further optimization harder.

While trying different mounting reagents for the ETC treated samples, I realized that glycerol does not give great results, even after very long incubations. ScaleA2 (4M Urea) works great on ETC treated brains, full transparency is achieved in just hours, but I'm afraid that it could disrupt the molecular integrity of the sample.

Could we try to design a home-made mounting reagent that would give similar results?

It seems that the best way to achieve index matching is to use a solution with ions presents at a high molarity. FocusClear(r) seems to use diatrizoic acid and meglumine to achieve that. Does anyone had any luck in making a good substitute?]]>
        </description>
    </item>
    <item>
        <title>program for movies</title>
        <link>https://forum.claritytechniques.org/discussion/189/program-for-movies</link>
        <pubDate>Mon, 29 Aug 2016 09:13:57 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>ron</dc:creator>
        <guid isPermaLink="false">189@/discussions</guid>
        <description><![CDATA[currently my row data images are tens of GB and the program i use can't upload them (Imaris). do you have any recommendation of which program is the one that you are working with or that you know can handle these amount of data? 
thanks.   ]]>
        </description>
    </item>
    <item>
        <title>a single neuron dye and image</title>
        <link>https://forum.claritytechniques.org/discussion/186/a-single-neuron-dye-and-image</link>
        <pubDate>Mon, 15 Aug 2016 13:00:36 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>ron</dc:creator>
        <guid isPermaLink="false">186@/discussions</guid>
        <description><![CDATA[I want to patch a neuron and fill it with fluorescent dye (Alexa fluor hydrazide 488, 50 uM) in 350 um slice and image it after CLARITY procedure. Can anyone tell me if this is possible to achieve?]]>
        </description>
    </item>
    <item>
        <title>Anyone using lightsheet microscope?</title>
        <link>https://forum.claritytechniques.org/discussion/180/anyone-using-lightsheet-microscope</link>
        <pubDate>Fri, 15 Apr 2016 17:47:23 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>JarekW</dc:creator>
        <guid isPermaLink="false">180@/discussions</guid>
        <description><![CDATA[Is anyone successfully using a lightsheet microscope with CLARITY and postmortem fixed tissue and if so, is it a commercial one such as the Zeiss Z1, homemade (openspim.org), modified light microscope such as http://www.jove.com/video/51342/setting-up-simple-light-sheet-microscope-for-toto-imaging-c-elegans  
or a different one?

I'm trying to figure out which would be the most appropriate approach, based on pricing, working distance, magnification range, number of lasers available, specimen size range (starting with 1cm cube), speed, and optics knowledge required.  Openspim requires 3d printing and machining parts which are not readily available from Thor etc, the commercial ones are I assume the most expensive (by how much?), and modifying a light scope such as an axiophot even when it already includes a powered stage and software may present technical limitations due to the already existing vertical axis and stage which may interfere with the illumination path.

Thank you
Jarek
]]>
        </description>
    </item>
    <item>
        <title>Increasing Z-stack range</title>
        <link>https://forum.claritytechniques.org/discussion/174/increasing-z-stack-range</link>
        <pubDate>Tue, 01 Dec 2015 20:34:24 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>LiamOLeary</dc:creator>
        <guid isPermaLink="false">174@/discussions</guid>
        <description><![CDATA[Hi,

I am trying to perform confocal 20X Z-stacks for the entire z-axis of 2-3mm thick, coronal adult mouse brain slices using 85% glycerol as mounting solution. I have been using a blutack to rest a coverslip on a slide with the slice. I have never had trouble with hydrogel embedding using a dessicator and mineral oil, or clearing using a hybridization oven and daily washes.

Normally, I can only see approximately 800um deep into the slice if I don't preincubate the section in glycerol (the objective lens can be lowered further, but it doesn't give a good signal). The other day, I left a slice in a 15mL tube containing glycerol for about 36 hours, and managed to get 2000um deep (I am using a fancy objective lens designed for SCALE meant to have a large working distance).   

Does anyone know of factors or methods which increase or decrease the depth to which one can image in thick sections of cleared tissue?

Thanks,
Liam]]>
        </description>
    </item>
    <item>
        <title>getting objectives for COLM</title>
        <link>https://forum.claritytechniques.org/discussion/172/getting-objectives-for-colm</link>
        <pubDate>Mon, 12 Oct 2015 17:55:37 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>jsdaniel</dc:creator>
        <guid isPermaLink="false">172@/discussions</guid>
        <description><![CDATA[Hello everyone, can anybody comment on how they procured the objectives mentioned in the COLM paper?  It appears that Olympus won't currently sell the imaging objective except together with their confocal systems.

I'm with a company called Applied Scientific Instrumentation that makes "microscope LEGOs".  We have developed a light sheet microscope adapted for smaller objects (see http://dispim.org/).  Several groups are interested in using our pieces to build a COLM, but the sticking point seems to be obtaining the objectives.

Any ideas?]]>
        </description>
    </item>
    <item>
        <title>COLM Imaging Locations</title>
        <link>https://forum.claritytechniques.org/discussion/171/colm-imaging-locations</link>
        <pubDate>Thu, 01 Oct 2015 21:54:53 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>NWASBY</dc:creator>
        <guid isPermaLink="false">171@/discussions</guid>
        <description><![CDATA[Hey guys!

My lab has successfully prepared and is in the process of preparing some full cleared rat brains and are looking for alternatives to confocal, etc. 

Does anyone in the area of VA/DC/MD area have an operational COLM set up? It would be greatly appreciated if we could gather some images from it.



]]>
        </description>
    </item>
    <item>
        <title>Mounting</title>
        <link>https://forum.claritytechniques.org/discussion/170/mounting</link>
        <pubDate>Fri, 11 Sep 2015 12:13:02 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>jose_jpr</dc:creator>
        <guid isPermaLink="false">170@/discussions</guid>
        <description><![CDATA[After clarification, I included the sample for two days in glycerol, but doesn't sink. Also, it shows a reduction in sample size. 

is it normal?]]>
        </description>
    </item>
    <item>
        <title>Mounting in glycerol</title>
        <link>https://forum.claritytechniques.org/discussion/29/mounting-in-glycerol</link>
        <pubDate>Thu, 18 Jul 2013 10:06:33 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>Fabio</dc:creator>
        <guid isPermaLink="false">29@/discussions</guid>
        <description><![CDATA[After ETC clearing my brain. I mounted it in 85% glycerol (v/v).
The brain was rotating in an incubator at 37°C for 2d.

After 1d the brain was almost completely clear. Just some spots inside looked opaque.

After 2d the brain became opaque.

I was expecting the opaque spots from day one were uncleared parts where the glycerol should diffuse,
but it was the other way around. The brain became opaque and just the outside parts look clarified.

Somebody had the same issue, or has an explanation?

I cleared my brain for 5 days at 37°C, following the protocol and with a standard chamber.]]>
        </description>
    </item>
    <item>
        <title>Huge background in cleared tissue</title>
        <link>https://forum.claritytechniques.org/discussion/157/huge-background-in-cleared-tissue</link>
        <pubDate>Thu, 26 Mar 2015 19:03:48 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>BJ2014</dc:creator>
        <guid isPermaLink="false">157@/discussions</guid>
        <description><![CDATA[Is it normal for background to be very bright for cleared brain sections (~2mm thick)?]]>
        </description>
    </item>
    <item>
        <title>CLARITY + iDISCO</title>
        <link>https://forum.claritytechniques.org/discussion/147/clarity-idisco</link>
        <pubDate>Wed, 28 Jan 2015 19:37:18 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>JAGS</dc:creator>
        <guid isPermaLink="false">147@/discussions</guid>
        <description><![CDATA[Is anyone doing iDISCO imaging with CLARITY or PACT samples?]]>
        </description>
    </item>
    <item>
        <title>3D printable chamber</title>
        <link>https://forum.claritytechniques.org/discussion/148/3d-printable-chamber</link>
        <pubDate>Mon, 02 Feb 2015 14:30:18 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>WFD</dc:creator>
        <guid isPermaLink="false">148@/discussions</guid>
        <description><![CDATA[Was wondering if anyone has created, and wouldn't mind sharing, a 3D chamber design for imaging on glass slides. This would be very helpful and offer a little more security than Blu-Tack when dealing with inverted microscopes. Thank you for any help.]]>
        </description>
    </item>
    <item>
        <title>Autofluorescence</title>
        <link>https://forum.claritytechniques.org/discussion/18/autofluorescence</link>
        <pubDate>Mon, 24 Jun 2013 02:51:00 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>KatherineHolzem</dc:creator>
        <guid isPermaLink="false">18@/discussions</guid>
        <description><![CDATA[For anyone who has gotten to imaging yet, have you noticed a lot of autofluorescence in the green and red wavelength ranges? I am working with heart tissue, which I know is notorious for autofluorescence, but sounds like this may be true for other tissues as well. To try to get around this, I am testing blue and far-red dyes, but I would like to know other thoughts or suggestions.

Also, according to the SeeDB article posted about by Bertrand_Vernay on the FocusClear discussion (http://forum.claritytechniques.org/discussion/1/focusclear#latest), this autofluorescence issue could be due to the Maillard reaction, which means it could potentially be prevented... however I don't think the chemicals used to do this would be practical to add to the ETC buffer during the clearing process (2-ME or 1-thiogylcerol). The Maillard reaction is reversible though.]]>
        </description>
    </item>
    <item>
        <title>3DISCO imaging setup / imaging chamber</title>
        <link>https://forum.claritytechniques.org/discussion/138/3disco-imaging-setup-imaging-chamber</link>
        <pubDate>Wed, 10 Dec 2014 19:08:55 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>fdavis</dc:creator>
        <guid isPermaLink="false">138@/discussions</guid>
        <description><![CDATA[Does anyone have any better (more leak-proof) alternative for imaging on an inverted confocal with the DISCO protocol (i.e. keeping in DBE, which is incompatible with almost everything!). We have tried a few brands of dental cement, which seem difficult/unreliable, although we haven't tried the Lang brand yet.

Is there an alternative solution we can image in? 

We just started the technique this week and may have cleared, antibody-stained tissue, but are not sure how to best image. 

Any suggestions very welcome!

Thanks,]]>
        </description>
    </item>
    <item>
        <title>Refractive index matching solution from Cargille Labs</title>
        <link>https://forum.claritytechniques.org/discussion/137/refractive-index-matching-solution-from-cargille-labs</link>
        <pubDate>Tue, 09 Dec 2014 18:11:36 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>Adam</dc:creator>
        <guid isPermaLink="false">137@/discussions</guid>
        <description><![CDATA[Has anyone tried the custom RI liquid from cargille labs (RI 1.454, cat no 1806Y) mentioned in the Tomer et al paper? Particularly, how does it compare to focus clear for imaging large samples, considering it is an order of magnitude cheaper?

Thanks!]]>
        </description>
    </item>
    <item>
        <title>Immunohistochemistry in the process</title>
        <link>https://forum.claritytechniques.org/discussion/125/immunohistochemistry-in-the-process</link>
        <pubDate>Wed, 08 Oct 2014 10:32:40 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>JAGS</dc:creator>
        <guid isPermaLink="false">125@/discussions</guid>
        <description><![CDATA[Hello,

In the CLARITY's process, When and How should I do the immunolocalization? Is there any protocol to do it?
I thing I should hatch it when it's clarified, is it correct? Can anyone guide me?

]]>
        </description>
    </item>
    <item>
        <title>Refractive index mismatch in confocal</title>
        <link>https://forum.claritytechniques.org/discussion/126/refractive-index-mismatch-in-confocal</link>
        <pubDate>Thu, 09 Oct 2014 13:41:06 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>LinusMG</dc:creator>
        <guid isPermaLink="false">126@/discussions</guid>
        <description><![CDATA[Hello everyone,

I was wondering whether there are any easy solutions for the refractive index mismatch when using general air or water-immersion objectives in confocal set-ups.
In SPIM set-ups this is easy to correct, at the end using one lens the light can be re-focused.
By now in confocal this issue seems to be solved using multi-immersion lenses or refractive-index matched objectives.

Does anyone know any generic correction collars that could be attached to any objective? 
Or have anyone came up with a nice solution?]]>
        </description>
    </item>
    <item>
        <title>Neurolucida and Fluoview FV10i - (or general imaging help)</title>
        <link>https://forum.claritytechniques.org/discussion/124/neurolucida-and-fluoview-fv10i-or-general-imaging-help</link>
        <pubDate>Tue, 07 Oct 2014 21:06:54 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>Clarifier</dc:creator>
        <guid isPermaLink="false">124@/discussions</guid>
        <description><![CDATA[Does anyone have experience imaging clarified tissues with either of these machines? If not, maybe you can help me anyway?

I'm having significant issues getting clear and focused images. The brain section I'm using is ~500μm, and Hoechst stained. It was passively cleared in a water bath (37°C) for about 6-8 weeks. 

There was endogenous GFP (d2GFP), but that seems to have degraded or washed out. My PI is concerned that the cells degraded after 2-3 months of waiting time.  I think my issue lies in mounting and with the FocusClear. I've been using a slide and cover slip (with bluetack), and the results have been less than impressive. 
https://drive.google.com/folderview?id=0B18lHiLR9KLTYXJlV1FlMHZJbms&amp;usp=sharing

Any ideas? Thanks a lot!!]]>
        </description>
    </item>
    <item>
        <title>COLM for rapid and high-resolution imaging of intact brains and other tissues</title>
        <link>https://forum.claritytechniques.org/discussion/110/colm-for-rapid-and-high-resolution-imaging-of-intact-brains-and-other-tissues</link>
        <pubDate>Sat, 21 Jun 2014 20:56:20 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>raju</dc:creator>
        <guid isPermaLink="false">110@/discussions</guid>
        <description><![CDATA[Hi Folks,

I would like to introduce COLM (CLARITY Optimized Light-sheet Microscope) for high-speed imaging of large clarified samples at high resolution. 

At the least three major innovations were needed over the light sheet microscopy idea to make COLM a reality. The details are here:
http://www.nature.com/nprot/journal/v9/n7/full/nprot.2014.123.html
And, additional details will be added here:
http://clarityresourcecenter.com/COLM.html

COLM specs in brief:
* An entire mouse brain can be imaged in 3-4 hours at half a micron resolution, and in about a day at quarter of micron resolution (spine level details).
* A mouse brain is about 3 TB of raw data at half a micron resolution, and about 10 TB at quarter micron. Therefore, COLM does real-time data compression (4-5 fold loss-less compression).
* In current version, a tissue of 1.4 cm x 1.4 cm x 4.5 cm size can be imaged at quarter of micron resolution.
* Current version can image up to 4 colors in one sample. 6 LASER engine is suggested in the current design.
* A very advanced, intuitive and easy-to-use control software (more or less a push-button system).

A conscious effort was made to develop COLM with off-the-shelf parts. Very minimum custom manufacturing needed. Current cost is estimated at less than 400K (excluding control software, which we will provide free-of-cost), and will become cheaper. I would estimate a system assembly time of a few days, once all parts are available.

Although I will be very happy to help spread the technology, I do realize that many labs may not be equipped for custom-built COLM. Therefore, currently exploring commercialization options to make it easily accessible and even more easier to use, provided there is enough interest.

As far as I know there is no other system that can image as large a sample at as high-resolution in as quick time as COLM.

Thanks,

Raju Tomer]]>
        </description>
    </item>
    <item>
        <title>Microscopy</title>
        <link>https://forum.claritytechniques.org/discussion/34/microscopy</link>
        <pubDate>Wed, 24 Jul 2013 13:44:18 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>aysegul</dc:creator>
        <guid isPermaLink="false">34@/discussions</guid>
        <description><![CDATA[Hi everybody,
I wanted also to  an important point about imaging and the need to find alternative imaging technique. Which is the best compatible microscope for Clarity?  (Light sheet microscopy (Single plane illumination), multi-photon laser microscopy, confocal microscopy, 2-photon laser microscopy). Is it possible to image the sample without confocal microscopy ?  Which microscopy can we use for displaying 3D?
Thanks in advance for your feedback and suggestions.
]]>
        </description>
    </item>
    <item>
        <title>Optical Projection Tomography</title>
        <link>https://forum.claritytechniques.org/discussion/63/optical-projection-tomography</link>
        <pubDate>Tue, 08 Oct 2013 15:47:29 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>KatherineHolzem</dc:creator>
        <guid isPermaLink="false">63@/discussions</guid>
        <description><![CDATA[Does anyone currently have (or is in the process of constructing) an OPT system? My PI told me about this imaging method, and now we are hoping to build one for our department. So if anybody has any pointers, that would be great. Seems like potentially one of the better methods for large-sample imaging with clear tissue, but has mostly been used for developmental/embryonic imaging since it came out &gt;10 years ago.

If you don't know about OPT, there are a few great papers out there. I have cited a couple below.

The original OPT publication: Sharpe et al. Science. 2002.
A recent publication about constructing your own OPT imaging system: Wong et al. PLOSone. 2013.]]>
        </description>
    </item>
    <item>
        <title>focusclear deposit</title>
        <link>https://forum.claritytechniques.org/discussion/70/focusclear-deposit</link>
        <pubDate>Sat, 26 Oct 2013 04:11:52 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>yetiti</dc:creator>
        <guid isPermaLink="false">70@/discussions</guid>
        <description><![CDATA[The recent batches of focusclear tends to form white deposit within the brain (particularly in ventricle). This is happening more and more often (and fast, ranging from several hours to 1-2 days). Does anyone have a good way to avoid this? I have tried "mountclear" from the same company, for post-focusclear mounting but did not have much improvement unfortunately. ]]>
        </description>
    </item>
    <item>
        <title>Microscopy Setups - What works best?</title>
        <link>https://forum.claritytechniques.org/discussion/48/microscopy-setups-what-works-best</link>
        <pubDate>Sat, 10 Aug 2013 11:59:39 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>SVSUNEURO</dc:creator>
        <guid isPermaLink="false">48@/discussions</guid>
        <description><![CDATA[Interested in hearing about microscopy/imaging solutions that you are all using. Please share your imaging setup and pros/cons of each. We are interested in brain tissue imaging at levels from systems/cells to synapses using multiple fluorophores (IH)? However, any general hints and tips would be appreciated.

What technologies work best for you folks? ]]>
        </description>
    </item>
    <item>
        <title>Imaging samples whose proteins could be denatured?</title>
        <link>https://forum.claritytechniques.org/discussion/89/imaging-samples-whose-proteins-could-be-denatured</link>
        <pubDate>Wed, 15 Jan 2014 17:32:20 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>patricia</dc:creator>
        <guid isPermaLink="false">89@/discussions</guid>
        <description><![CDATA[Hi everybody, I've cleared a kidney in the ETC chamber but during the weekend something happened with the electricity in the lab, and when I arrived the water pomp wasn't working, the power pac with error and the kidney had the renal fascia (the layer that covers the kidney) a little bit black, like burned. The thing is that the rest of the kidney seems to be well and transparent. Now I want to stain it, but I'm wondering if there is a possibility that the proteins of the kidney are denatured so I cannot get an specific staining, do you think it is possible? Thank you!]]>
        </description>
    </item>
    <item>
        <title>Scanning Time</title>
        <link>https://forum.claritytechniques.org/discussion/79/scanning-time</link>
        <pubDate>Fri, 06 Dec 2013 01:38:48 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>DominicJG</dc:creator>
        <guid isPermaLink="false">79@/discussions</guid>
        <description><![CDATA[Hello,

I was wondering if anyone has experience or an idea how long it takes to scan an entire brain? In addition, what software was used? There is an freeware available that seems to be promising: www.vaa3d.org

Thank you for everyone's ideas.]]>
        </description>
    </item>
    <item>
        <title>We finally got it to work with viral injection.</title>
        <link>https://forum.claritytechniques.org/discussion/72/we-finally-got-it-to-work-with-viral-injection</link>
        <pubDate>Wed, 13 Nov 2013 15:16:55 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>LauraLynch</dc:creator>
        <guid isPermaLink="false">72@/discussions</guid>
        <description><![CDATA[https://drive.google.com/file/d/0B5H6exz8a5XARmQtR25QMWFKNUk/edit?usp=sharing

This is a Thy1EYFP mouse cerebellum in which GCaMP6f (EGFP) was injected into the simplex/crus1 area via adeno-associated virus (AAV).  The large cells are Purkinje cells (GFP).  The paler cells in the center are mossy fibers (EYFP).

The brain was fixed in hydrogel overnight, then passively cleared in 50 ml of clearing solution in a 37 degree water bath, with almost daily solution changes, for 16 days.  All but the white matter had cleared at this point.  We used FocusClear (about 5 ml for the right hemisphere; the solution had been used briefly twice before).  The hemisphere was in FocusClear for about 20 hours before imaging.

We used a 20x Zeiss lens (nothing special) on a 2-photon microscope and were able to resolve structures down to 1 mm.]]>
        </description>
    </item>
    <item>
        <title>VECTASHIELD Mounting Media</title>
        <link>https://forum.claritytechniques.org/discussion/45/vectashield-mounting-media</link>
        <pubDate>Wed, 07 Aug 2013 21:07:56 +0000</pubDate>
        <category>Sample Imaging</category>
        <dc:creator>zhanx</dc:creator>
        <guid isPermaLink="false">45@/discussions</guid>
        <description><![CDATA[Has anybody tried VECTASHIELD Mounting Media to match the RI? In their website, their media has RI around 1.45, and it's cheaper than FocusClear. Not sure if it's a good option.]]>
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