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        <title>General — CLARITY forum</title>
        <link>https://forum.claritytechniques.org/</link>
        <pubDate>Sat, 08 Aug 2026 00:39:40 +0000</pubDate>
        <language>en</language>
            <description>General — CLARITY forum</description>
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    <item>
        <title>Would freezing a CLARITY brain be possible?</title>
        <link>https://forum.claritytechniques.org/discussion/217/would-freezing-a-clarity-brain-be-possible</link>
        <pubDate>Tue, 09 May 2023 18:00:43 +0000</pubDate>
        <category>General</category>
        <dc:creator>wkenkel</dc:creator>
        <guid isPermaLink="false">217@/discussions</guid>
        <description><![CDATA[For reasons too complicated to get into, I'm looking to slice some CLARITY brain tissue at 40 microns. Typically, I would use a cryostat for slicing fixed brain tissue, but I don't know whether freezing a hydrogel embedded brain would damage the tissue. Does anyone have insight / experience with this? Thanks!]]>
        </description>
    </item>
    <item>
        <title>What Challenges with CLARITY have you had?</title>
        <link>https://forum.claritytechniques.org/discussion/216/what-challenges-with-clarity-have-you-had</link>
        <pubDate>Wed, 30 Jun 2021 16:21:52 +0000</pubDate>
        <category>General</category>
        <dc:creator>ClearLightBio</dc:creator>
        <guid isPermaLink="false">216@/discussions</guid>
        <description><![CDATA[Have you tried applying CLARITY?  What tissue or organism have you had difficulty with in applying CLARITY?]]>
        </description>
    </item>
    <item>
        <title>Bibliographical references for combination active-passive CLARITY</title>
        <link>https://forum.claritytechniques.org/discussion/215/bibliographical-references-for-combination-active-passive-clarity</link>
        <pubDate>Wed, 01 Jul 2020 14:54:31 +0000</pubDate>
        <category>General</category>
        <dc:creator>Tilo</dc:creator>
        <guid isPermaLink="false">215@/discussions</guid>
        <description><![CDATA[Hi everyone, I have read in this forum that the best approach to obtain maximum transparency without damaging the sample is to combine passive and active CLARITY... The protocol was very well described, but I would need some bibliographical reference of that, and the page seems no more available...
Can someone help me?
Thanks in advance]]>
        </description>
    </item>
    <item>
        <title>Is it possible to over-clear your tissue?</title>
        <link>https://forum.claritytechniques.org/discussion/213/is-it-possible-to-over-clear-your-tissue</link>
        <pubDate>Tue, 21 May 2019 17:59:48 +0000</pubDate>
        <category>General</category>
        <dc:creator>aicilalane</dc:creator>
        <guid isPermaLink="false">213@/discussions</guid>
        <description><![CDATA[I'm clearing whole brains and spinal cords from adult mice, passively. It seems to be going well so far- it's been about a month and there is definitely clearing happening. My question has to do with whether it is possible to "over"clear tissue with CLARITY. In my samples, the clearing isn't necessarily even across the tissue; obviously with regard to depth the outer regions will clear faster than the middle, but there are also a few areas that seem to have minimal clearing in a spinal cord that is almost entirely clear elsewhere (possibly because I didn't remove the dura). Should I be worried about leaving those mostly-cleared samples at 37C for the time it takes for those scattered areas to become clear? (Does that risk any damage to the areas that have already cleared?) Thanks!]]>
        </description>
    </item>
    <item>
        <title>Critical details of the protocol</title>
        <link>https://forum.claritytechniques.org/discussion/93/critical-details-of-the-protocol</link>
        <pubDate>Fri, 31 Jan 2014 13:51:55 +0000</pubDate>
        <category>General</category>
        <dc:creator>LinusMG</dc:creator>
        <guid isPermaLink="false">93@/discussions</guid>
        <description><![CDATA[Hello everyone,

I am trying for the first time the CLARITY protocol as a part of my recently started PhD project. Since some months ago we have been gathering all the needed material and from approximately three weeks ago we started with 4 perfusions. Until today it seemed it was going good enough unless for two bubbles in the ventricles. Today we have looked for fluorescence in our first sample (in ScaleU2) but we couldn't see any signal, maybe because of a not long enough ETC clearing step.

Implementing the protocol with the first brain I have come up with two critical doubts:

 - Pump flow rate: We are using a Lauda Eco RE 415. I started using a ~15L/min (At 37ºC and 25V) flow rate in order to avoid having bubbles in the inlet of the ETC chamber. After 8 days I switched to a slower flow rate (~10L/min). I noticed that using the slower flow rate clearing seemed to be more efficient. 
(If anyone is using the same pump I chose the settings 3 and then 2 in the pump power menu.)

My question here is: there is any agreement about the optimal flow rate for a range of settings between 20-30V and at 37ºC? @joelrosiene suggested to use flow rates lower than 180mL/min. @nicolasrenier reports big bubbles trapped in the ventricles using the maximum flow rate allowed by Lauda (maybe caused by a not gentle start after setting the sample into the chamber?). Also @Neon reports 48hrs ETC using 20-30ml/min and 30V. 
A second question is: Has anybody used successfully the maximum values suggested in the original article (50ºC and 60V)?

- Mounting media for imaging: We decided to use ScaleU2 after reading the advances by @LauraLynch using Fauxcusclear. Anyway @joelrosiene also reports loss of signal using ScaleU2 (could it be that the slower flow rate that we used has something to do with the loss of signal?) .

@LauraLynch could you confirm that you don't have loss of signal using ScaleU2? 
@nicolasrenier did you have any luck with other recipes following the FocusClear patent? 
@Neon did you successfully image your 48hrs cleared samples?

Thank you all for your insightful contributions in this forum.



P.S.: A link for some pictures of our setup and sample:
https://plus.google.com/photos/109959696841588744124/albums/5975050760506825313?authkey=CIGZwO717-n_OA

We have been running ETC clearing for 11 days and probably I have been too impatient washing and incubating in ScaleU2 (the brain was translucent but not very clear).]]>
        </description>
    </item>
    <item>
        <title>CLARITY wiki is down</title>
        <link>https://forum.claritytechniques.org/discussion/210/clarity-wiki-is-down</link>
        <pubDate>Sat, 13 Oct 2018 01:31:04 +0000</pubDate>
        <category>General</category>
        <dc:creator>Sejin</dc:creator>
        <guid isPermaLink="false">210@/discussions</guid>
        <description><![CDATA[It has been down for a few days. Does anyone know when it will be back online?]]>
        </description>
    </item>
    <item>
        <title>Clarity Wiki Down?</title>
        <link>https://forum.claritytechniques.org/discussion/204/clarity-wiki-down</link>
        <pubDate>Thu, 15 Feb 2018 23:46:44 +0000</pubDate>
        <category>General</category>
        <dc:creator>EHubb</dc:creator>
        <guid isPermaLink="false">204@/discussions</guid>
        <description><![CDATA[Hello,

I was just hoping to find out if anyone knew that status of the clarity Wiki as it appears to have been down for the last couple of days.
]]>
        </description>
    </item>
    <item>
        <title>McMaster-Carr for Europe</title>
        <link>https://forum.claritytechniques.org/discussion/117/mcmaster-carr-for-europe</link>
        <pubDate>Sat, 19 Jul 2014 08:07:26 +0000</pubDate>
        <category>General</category>
        <dc:creator>JAGS</dc:creator>
        <guid isPermaLink="false">117@/discussions</guid>
        <description><![CDATA[Is there any online shop in Europe to buy all the materials of McMaster-Carr and that it was cheap? ]]>
        </description>
    </item>
    <item>
        <title>Collaboration on CLARITY</title>
        <link>https://forum.claritytechniques.org/discussion/202/collaboration-on-clarity</link>
        <pubDate>Fri, 01 Dec 2017 20:17:00 +0000</pubDate>
        <category>General</category>
        <dc:creator>pricee</dc:creator>
        <guid isPermaLink="false">202@/discussions</guid>
        <description><![CDATA[Colleagues- my lab is interested in in vivo brain tissue engineering.  Part of our methodology involves implanting fibrin cylinders (6 mm x 0.7 mm) into rat brain (live) and asking if, after 8-12 weeks, do the implants create new neural migratory paths.  We do not have the instrumentation to an analyze brains using CLARITY and am sending out a broad request for a collaborator who can assist in our study.
Sincerely,
Elmer Price]]>
        </description>
    </item>
    <item>
        <title>CLARITY training workshops</title>
        <link>https://forum.claritytechniques.org/discussion/194/clarity-training-workshops</link>
        <pubDate>Fri, 03 Mar 2017 18:55:54 +0000</pubDate>
        <category>General</category>
        <dc:creator>Kristin_Engberg</dc:creator>
        <guid isPermaLink="false">194@/discussions</guid>
        <description><![CDATA[Hi everyone,

I just wanted to send a reminder that the Deisseroth lab offers training workshops on the CLARITY technique if you'd like a chance to learn and troubleshoot in-person.  More information can be found on the CLARITY resource center website:  http://clarityresourcecenter.org/]]>
        </description>
    </item>
    <item>
        <title>ETT in EDC fixation for RNA</title>
        <link>https://forum.claritytechniques.org/discussion/193/ett-in-edc-fixation-for-rna</link>
        <pubDate>Thu, 19 Jan 2017 11:53:03 +0000</pubDate>
        <category>General</category>
        <dc:creator>Iana</dc:creator>
        <guid isPermaLink="false">193@/discussions</guid>
        <description><![CDATA[ETT is supposed to be a crosslinker. Does anyone know the chemistry behind? where it binds?]]>
        </description>
    </item>
    <item>
        <title>VA-044, PEA-Clarity protocols on Arabidopsis thaliana</title>
        <link>https://forum.claritytechniques.org/discussion/192/va-044-pea-clarity-protocols-on-arabidopsis-thaliana</link>
        <pubDate>Tue, 25 Oct 2016 11:53:09 +0000</pubDate>
        <category>General</category>
        <dc:creator>Paola_Puggioni</dc:creator>
        <guid isPermaLink="false">192@/discussions</guid>
        <description><![CDATA[Hi guys!

I will soon start to use the clarity protocol on plants (A.thaliana).
Some of you have some experience in that and can give me some suggestion?

I have some doubts about the initiator VA-044, is it true that is explosive? how usually do you store it? 

Cheers,

Paola]]>
        </description>
    </item>
    <item>
        <title>Sucrose</title>
        <link>https://forum.claritytechniques.org/discussion/188/sucrose</link>
        <pubDate>Sun, 21 Aug 2016 07:21:20 +0000</pubDate>
        <category>General</category>
        <dc:creator>ron</dc:creator>
        <guid isPermaLink="false">188@/discussions</guid>
        <description><![CDATA[does anyone use CLARITY protocol on tissue which was in Sucrose solution for long period? do you know of any reactivity between the Hydorgel solution and the Sucrose? ]]>
        </description>
    </item>
    <item>
        <title>Tissue Sectioning AFTER clearing</title>
        <link>https://forum.claritytechniques.org/discussion/184/tissue-sectioning-after-clearing</link>
        <pubDate>Tue, 14 Jun 2016 14:46:09 +0000</pubDate>
        <category>General</category>
        <dc:creator>balsorjl</dc:creator>
        <guid isPermaLink="false">184@/discussions</guid>
        <description><![CDATA[Has anyone tried sectioning tissue AFTER clearing? I have seen some groups that section tissue after acrylamide hydrogel incubation and polymerization, but I would like to section after tissue has cleared completely. 

First, I am trying to avoid freezing cleared tissue. Second, when I mount my samples to a microslicer for sectioning, my adhesive is absorbed into the entire block of tissue. 

Suggestions?]]>
        </description>
    </item>
    <item>
        <title>Use of CLARITY on tumors</title>
        <link>https://forum.claritytechniques.org/discussion/185/use-of-clarity-on-tumors</link>
        <pubDate>Wed, 15 Jun 2016 05:22:07 +0000</pubDate>
        <category>General</category>
        <dc:creator>dvramater</dc:creator>
        <guid isPermaLink="false">185@/discussions</guid>
        <description><![CDATA[Has anybody used the CLARITY technique on tumors?  My lab is investigating nerve growth into tumors and are wondering  which technique (CLARITY, CUBIC, 3DISCO etc...) is preferred by other researchers?

TIA!]]>
        </description>
    </item>
    <item>
        <title>Tissue Storage after clearing</title>
        <link>https://forum.claritytechniques.org/discussion/130/tissue-storage-after-clearing</link>
        <pubDate>Fri, 14 Nov 2014 14:15:40 +0000</pubDate>
        <category>General</category>
        <dc:creator>balsorjl</dc:creator>
        <guid isPermaLink="false">130@/discussions</guid>
        <description><![CDATA[Can anyone recommend a better tissue storage technique for after clearing than PBS or PBS-T at room temp? I find the sample continues to swell and the hydrogel collapses when left in this solution for too long.]]>
        </description>
    </item>
    <item>
        <title>FocusClear Alternative</title>
        <link>https://forum.claritytechniques.org/discussion/96/focusclear-alternative</link>
        <pubDate>Mon, 24 Feb 2014 21:09:00 +0000</pubDate>
        <category>General</category>
        <dc:creator>Arun1982</dc:creator>
        <guid isPermaLink="false">96@/discussions</guid>
        <description><![CDATA[Does anyone have an working alternative to Focus Clear solution. ]]>
        </description>
    </item>
    <item>
        <title>Rapiclear-confocal microscopy</title>
        <link>https://forum.claritytechniques.org/discussion/173/rapiclear-confocal-microscopy</link>
        <pubDate>Fri, 30 Oct 2015 06:24:22 +0000</pubDate>
        <category>General</category>
        <dc:creator>Bella</dc:creator>
        <guid isPermaLink="false">173@/discussions</guid>
        <description><![CDATA[Hi 
GFP tagging virus was injected in the rat brain and after 3 weeks, rat was purfused.
I sliced brain tissue in 1mm thickness and 
cleared with Rapiclear1.47 for several days. 
Also, mounted the sample with iSpacer and Rapiclear solution. 
However, when I tried to image the sampel with confocal microscopy (olympus) 100x in depth,
focus was not fixed and the result was blurry-greenish image. 

I am not sure whether the sample was a problem(not cleared enough) or virus was the problem. 
White matter was cleared in a yellowish color but the gray matter was very evident.

Could you share your opinion on this?
Thanks 
]]>
        </description>
    </item>
    <item>
        <title>CLARITY and FISH</title>
        <link>https://forum.claritytechniques.org/discussion/16/clarity-and-fish</link>
        <pubDate>Sun, 23 Jun 2013 16:13:35 +0000</pubDate>
        <category>General</category>
        <dc:creator>Claire_Zhang</dc:creator>
        <guid isPermaLink="false">16@/discussions</guid>
        <description><![CDATA[Technically, could the tissue went through CLARITY be used for FISH (Fluorescence in situ hybridization)? As far as I know the size of a regular DNA probe is smaller than that of a common antibody. Would the hydrogel fit for the other conditions required for FISH?  What are the precautions would be? Thank you!]]>
        </description>
    </item>
    <item>
        <title>Clearing of postmortem human brain tissue</title>
        <link>https://forum.claritytechniques.org/discussion/86/clearing-of-postmortem-human-brain-tissue</link>
        <pubDate>Thu, 09 Jan 2014 23:58:47 +0000</pubDate>
        <category>General</category>
        <dc:creator>Anke</dc:creator>
        <guid isPermaLink="false">86@/discussions</guid>
        <description><![CDATA[I was wondering if there are users on this forum that try to clear human postmortem brain tissue. In the paper it is stated that previous formalin-stored material (more than 6 yrs in formalin) was still suitable for CLARITY. I used Saponin in the hydrogel and tried passive clearing for a month on long-fixed (&gt;1 yr) and short fixed (72hrs) material and there seems to be a large difference in clearing of the samples, where no clearing has been observed in 200 um long-fixed material compared to (beginning of) clearing of 3 mm chunck of short-fixed material. 

Does anybody have similar experiences? Would it be advisable to switch to ETC for long-fixed material?

Thanks!
Anke]]>
        </description>
    </item>
    <item>
        <title>Sectioning human spinal cord</title>
        <link>https://forum.claritytechniques.org/discussion/167/sectioning-human-spinal-cord</link>
        <pubDate>Mon, 15 Jun 2015 12:42:47 +0000</pubDate>
        <category>General</category>
        <dc:creator>MRGneuro</dc:creator>
        <guid isPermaLink="false">167@/discussions</guid>
        <description><![CDATA[Hi All,

Today I attempted to section some human spinal cord that had been embedded in the hydrogel on a vibratome. I attempted to get sections of 250um thickness but found it rather difficult and the tissue was rather resistant to be being cut even at slow speeds. Has anyone else had this issue and/or does any have suggestions to make it easier?

Thanks]]>
        </description>
    </item>
    <item>
        <title>Using Clarity for Liver tissue</title>
        <link>https://forum.claritytechniques.org/discussion/103/using-clarity-for-liver-tissue</link>
        <pubDate>Mon, 31 Mar 2014 14:28:12 +0000</pubDate>
        <category>General</category>
        <dc:creator>Vortexam</dc:creator>
        <guid isPermaLink="false">103@/discussions</guid>
        <description><![CDATA[Hi,I am also trying to make liver tissue transparent.I have few questions?
A. what type of tissue one can use in case of liver, freshly dissected or formalin-PFA stored tissue?
B. Has someone already tried using this technique to make liver tissue transparent? Any tips or problems faced?
C. Does the liver need to be sliced into sections of 200um thick or an entire liver lobe can be used?]]>
        </description>
    </item>
    <item>
        <title>Spine Swelling</title>
        <link>https://forum.claritytechniques.org/discussion/169/spine-swelling</link>
        <pubDate>Thu, 06 Aug 2015 21:22:45 +0000</pubDate>
        <category>General</category>
        <dc:creator>BJ2014</dc:creator>
        <guid isPermaLink="false">169@/discussions</guid>
        <description><![CDATA[I'm imaging mouse cortical neurons expressing GFP, and noticed that the spines are pretty large compared to uncleared spines. Is swelling an expected side effect? I can't find anything in the literature about spine swelling. All feedback is greatly appreciated!]]>
        </description>
    </item>
    <item>
        <title>How long does ScaleU2 take to work?</title>
        <link>https://forum.claritytechniques.org/discussion/168/how-long-does-scaleu2-take-to-work</link>
        <pubDate>Thu, 06 Aug 2015 07:22:52 +0000</pubDate>
        <category>General</category>
        <dc:creator>Twigs</dc:creator>
        <guid isPermaLink="false">168@/discussions</guid>
        <description><![CDATA[I have E13.5 embryos which have been in ScaleU2 solution for 4 days now (after A2 and B4) and I haven't noticed any clearing whatsoever. Shouldn't I see some transparancy by now?]]>
        </description>
    </item>
    <item>
        <title>CLARITY Cost Optimization</title>
        <link>https://forum.claritytechniques.org/discussion/61/clarity-cost-optimization</link>
        <pubDate>Wed, 02 Oct 2013 02:23:19 +0000</pubDate>
        <category>General</category>
        <dc:creator>ecahill</dc:creator>
        <guid isPermaLink="false">61@/discussions</guid>
        <description><![CDATA[Hi Everyone,

As an undergraduate engineering senior design project, we have been looking at potential for optimization of the CLARITY protocol, in terms of both time and cost.  I thought I would try to get input here on what areas you would like to see explored as we spend the year working on this project.  Are there particular areas that take far too long or that cost too much? We have been hearing from others that the FocusClear solution, the platinum electrodes, and the power supply are areas that we can work on. Any suggestions you have would be greatly appreciated. Of course we'll share anything useful that we find, so think of this as an opportunity to get us to explore these things for you. 

Thanks!]]>
        </description>
    </item>
    <item>
        <title>Iodine staining - STABILITY</title>
        <link>https://forum.claritytechniques.org/discussion/164/iodine-staining-stability</link>
        <pubDate>Tue, 05 May 2015 04:10:40 +0000</pubDate>
        <category>General</category>
        <dc:creator>acarlisle</dc:creator>
        <guid isPermaLink="false">164@/discussions</guid>
        <description><![CDATA[Hello, 

Just wondering if anyone is working with the STABILITY protocol?  The protocol uses the stabilisation aspect of CLARITY, but instead of lipid clearing after gel polymerisation, the samples are iodine stained and CT scanned.

I am starting to use STABILITY in my work and it would be great to discuss any issues that arise with others!

This is the protocol paper if anyone is interested: Structural Stabilization of Tissue for Embryo Phenotyping Using Micro-CT with Iodine Staining by Wong et al. 2013. 

Thanks!]]>
        </description>
    </item>
    <item>
        <title>Anyone have an archive of the CLARITY wiki?</title>
        <link>https://forum.claritytechniques.org/discussion/160/anyone-have-an-archive-of-the-clarity-wiki</link>
        <pubDate>Sun, 05 Apr 2015 20:41:15 +0000</pubDate>
        <category>General</category>
        <dc:creator>hydrazine</dc:creator>
        <guid isPermaLink="false">160@/discussions</guid>
        <description><![CDATA[Seems to be down, anyone know how to access info on there?]]>
        </description>
    </item>
    <item>
        <title>Clarification methods in Spain</title>
        <link>https://forum.claritytechniques.org/discussion/163/clarification-methods-in-spain</link>
        <pubDate>Tue, 21 Apr 2015 11:00:17 +0000</pubDate>
        <category>General</category>
        <dc:creator>jose_jpr</dc:creator>
        <guid isPermaLink="false">163@/discussions</guid>
        <description><![CDATA[Anyone working with clarification methods and SPIM microscope in Spain?
]]>
        </description>
    </item>
    <item>
        <title>drop fixation for CLARITY</title>
        <link>https://forum.claritytechniques.org/discussion/162/drop-fixation-for-clarity</link>
        <pubDate>Tue, 14 Apr 2015 13:51:53 +0000</pubDate>
        <category>General</category>
        <dc:creator>jburn</dc:creator>
        <guid isPermaLink="false">162@/discussions</guid>
        <description><![CDATA[Has anyone drop fixed brains for CLARITY instead of perfusing? I have neonatal brains that I would prefer to drop fix instead of perfuse but am worried it won't work? If you've done this, does it work and how long did you drop fix them (and did you do acrylamide and PFA or just PFA initially?).  Our lab uses the PACT/PARS protocol.  ]]>
        </description>
    </item>
    <item>
        <title>My brain is White!</title>
        <link>https://forum.claritytechniques.org/discussion/146/my-brain-is-white</link>
        <pubDate>Thu, 22 Jan 2015 10:21:51 +0000</pubDate>
        <category>General</category>
        <dc:creator>JAGS</dc:creator>
        <guid isPermaLink="false">146@/discussions</guid>
        <description><![CDATA[After 24h in the storage solution (PBST (0.1% Triton X) + Azide Sodium) my sample is white. I think that it's due to the detergent's precipitate. Could you help me? Had it happened to you anytime? ]]>
        </description>
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