Cheap alternative oil and sealing glue resistant to BABB

[Etai Sapoznik]

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Dear all,
We are looking to use oil for refractive index matching with BABB. We need large quantities (several tens of mililiters for each run), so oils from Cargille are too expensive. Are there any alternative sources?
Does anybody have experience with Ethyl cinnamate or Anethole? We would like to know how corrosive such oils are and if an objective would get damaged if we submerge it in such an immersion medium?
Lastly, we wanted to know if anyone has experience in using glue which is resistant to BABB so that one can permanently glue an optical window to a chamber that would contain BABB?​

Thank you in advance.

Etai Sapoznik

[Aleksander Szczurek]

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Dear Etai,
Ethyl Cinnamate is very smelly (it is an esther if I am not mistaken). The
smell becomes really tiring after a while.

Have you considered using high Histodenz in water as an immersion medium?
Check papers on SeeDB2 for more details.
Reftactive index should match your requirements. There might be a problem
though as the water may evaporate from the solution.

The other option could (I have never tried this one and have no idea about
its effect on scopes objective) be to use pure 2,2'-thiodiethanol (RI>1.52).

best
Aleks

2018-04-05 9:49 GMT-05:00 Etai Sapoznik <[hidden email]>:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
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> *****
>
> Dear all,
> We are looking to use oil for refractive index matching with BABB. We need
> large quantities (several tens of mililiters for each run), so oils from
> Cargille are too expensive. Are there any alternative sources?
> Does anybody have experience with Ethyl cinnamate or Anethole? We would
> like to know how corrosive such oils are and if an objective would get
> damaged if we submerge it in such an immersion medium?
> Lastly, we wanted to know if anyone has experience in using glue which is
> resistant to BABB so that one can permanently glue an optical window to a
> chamber that would contain BABB?​
>
> Thank you in advance.
>
> Etai Sapoznik
>

[Uwe Schroeer]

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Dear Etai,

in case of BABB cleared samples, as you know, one should avoid any contact with aqueous buffers for imaging. The sample has been completely dehydrated before index matching with BABB. As soon as the cleared sample gets in contact with some water containing liquids it will get milky again.
You have to meet the RI of 1.55-1.56 depending of the quality of the BABB. ECi suits perfectly. However it is indeed a bit smelly. An alternative would be Benzyl ether. Slightly less smelly. Please consider that this is an organic solvent and it is recommended to have a fume hood or a gas extraction device. However it is less harmful than BABB. You might check the safety documentation on a providers page like for instance Sigma-Aldrich (https://www.sigmaaldrich.com/catalog/product/aldrich/108014?lang=en&region=GB ).
Another alternative might be silicone oil and mineral oil. A mixture of both is used for CUBIC samples to image. For sure the RI is here lower about 1.47. I am not sure if an extended equilibration might be sufficient enough to overcome this issue. If you want to try please use the following oils (https://www.sigmaaldrich.com/catalog/search?term=M5904&interface=All&N=0&mode=match%20partialmax&lang=en&region=GB&focus=product  & https://www.sigmaaldrich.com/catalog/search?term=175633&interface=All&N=0&mode=match%20partialmax&lang=en&region=GB&focus=product ). There will be others for sure which will also work. Unfortunately once I mixed different oils and they became milky.
Another solution would be 2,2′-Thiodiethanol. It has a RI of about 1.52. I would absolutely not recommend to use it undiluted. The smell is extreme.
If you are looking for objective lenses which can stand all these solutions you might have a look at these: http://www.lavisionbiotec.com/products/objective-lenses.html
There is also a Leica 20x BABB objective lens with pretty nice features:
Obj. HCX APO L20x/0.95 IMM
Apochromat Immers  (ne= 1.563).
Transmission in VISIR: >85% in VIS & 90% in IR (800 nm)
WD: 1.95 mm.

With kind regards,

Uwe

[George McNamara]

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The mention of mineral oil in a previous reply led me to do a Google
search for: mineral oil refractive index

which turned up this hit:

(I note that "wintergreen oil" = methyl salicylate, another old school
clearing agent)

https://www.gemsociety.org/article/refractive-index-list-of-common-household-liquids


  Refractive Index List of Common Household Liquids

------------------------------------------------------------------------
*byInternational Gem Society
<https://www.gemsociety.org/author/internationalgemsociety/>*


      Question

/Your article ongemstones and refraction liquids
<https://www.gemsociety.org/article/gemstones-refraction-liquids/>has a
refractive index list for fluids frequently used ingemstone testing
<https://www.gemsociety.org/article/how-to-identify-gems/>. But many of
these are expensive and/or poisonous. Do you have a refractive index
list of common household liquids that can be used for immersions? I’ve
found information online for things like vegetable oils. Nevertheless,
I’d really like to see a definitive, accurate list of “everyday fluids”
that actual gemologists actually use. Also, do you have any preferences
or tips for using these refraction liquids?/


      Refractive Index List of Common Household Liquids

Liquid Refractive Index
alcohol, ethyl 1.36
almond oil 1.45-1.47
anise oil 1.54-1.56
Canadian balsam 1.53-1.55
cassia oil 1.58-1.60
castor oil 1.47-1.48
cedar wood oil 1.51
cinnamon oil 1.59-1.62
clove oil 1.53
coconut oil 1.43-1.46
cod liver oil 1.46-1.48
corn oil 1.47-1.48
cottonseed oil 1.45-1.48
eucalyptus oil 1.46-1.47
glycerol (glycerin oil) 1.47
kerosene 1.45
lanolin 1.48
lemon oil 1.47-1.48
linseed oil 1.47-1.49
mineral oil 1.47-1.48
neatsfoot oil 1.47
olive oil 1.44-1.47
palm oil 1.44-1.46
peppermint oil 1.46-1.47
rape seed oil 1.47-1.48
safflower oil 1.47-1.48
sandalwood oil 1.50-1.51
sesame oil 1.47
soybean oil 1.47-1.48
tung oil 1.49-1.52
turpentine 1.47
water 1.33
wintergreen oil 1.54

/Editor’s Note: This list was compiled from information provided by
Donald Clark, CSM IMG, Dr. Gerald Wykoff, Dr. Clive Washington, Roy
Kersey, and others./


      Vegetable Oil Variations

Be aware that vegetable oils have variable properties. Even oils made
from the same species of plant vary in chemical composition depending on
things like plant varieties, where the plant grew, how much sun it got,
etc. Nevertheless, most plant triglyceride oils (castor, corn, olive,
soybean, for example) have fairly similar RIs.Tung oil
<http://www.amazon.com/s/ref=nb_sb_noss_1?url=search-alias%3Daps&field-keywords=tung+oil>is
a little higher, but make sure it’s not adulterated. Clove oil
<http://www.amazon.com/s/ref=nb_sb_ss_c_0_9?url=search-alias%3Daps&field-keywords=clove+oil&sprefix=clove+oil%2Caps%2C294> is
quite a bit higher.

Dr. Clive Washington


      Refractol

Maybe it’s not quite a household liquid, but I use a product
calledRefractol
<http://www.kingsleynorth.com/skshop/product.php?id=90647&catID=1041>.
It’s clear, odorless, nontoxic, and has a listed RI of 1.567. If you buy
it online, double check the listed RI. Some product has an RI of 1.52 to
make it transparent to glass microscopic slides.

Keep in mind that oils do have variations in RI, and some household
liquids, like turpentine, can be noxious.

Donald Clark, CSM IMG


      Nail Polish Dryer

For looking into a stone under a microscope to findinclusions
<https://www.gemsociety.org/article/identifying-inclusions/>, I use a
product calledSally Hansen Dry Kwik
<http://www.amazon.com/Sally-Hansen-Color-Corrector-3097/dp/B001T8OD9Q/ref=sr_1_1?s=beauty&ie=UTF8&qid=1443359494&sr=1-1&keywords=Sally+Hansen+dry+kwik>.
It’s, of all things, nail polish dryer. In my opinion, it works better
than Refractol.

Harold


      Cinnamon Oil Pros and Cons

I myself usecinnamon oil
<http://www.amazon.com/s/ref=nb_sb_noss_1?url=search-alias%3Daps&field-keywords=cinnamon+oil>.
It has a pleasant, if strong, smell. Some warnings: it may eventually
eat through the seal of its jar and might produce red welts on you if
you get it on your face. (It did to me). Also, if you’re examining
rough, some gem dealers may not like you giving them back scented
stones. The dealers with whom I’ve done previous business have had no
objections to my immersing their rough. Ask first.

Scentless Refractol may be better for some, but cinnamon oil is almost
exactly the same RI astourmaline
<https://www.gemsociety.org/article/tourmaline-jewelry-and-gemstone-information/>andtopaz
<http://www.gemsociety.org/article/topaz-jewelry-and-gemstone-information/>.
It would be quite good withspinel
<http://www.gemsociety.org/article/spinel-jewelry-and-gemstone-information/>andcorundum
<https://www.gemsociety.org/article/corundum-jewelry-gemstone-information/>,
too. Cinnamon oil does have a yellow color, so those who want absolutely
clear fluid will have to look for something else.

Roy Kersey


***

another web hit, another table, this with one form of Silicone Oil
(another is whatever Olympus sells for its S.I. oil lenses, 1.405 ...
see also Boothe et al 2017 Elife for mixing OptiPrep (Iodixanol, 50%
solution in water is available from Sigma-Aldrich. D-1556 $243 for 250
mL ... just missed out on a fun April Fool's joke opportunity for tissue
culturists using phase contrast microscope) ~1:1 with cell culture media
to get to RI 1.36 ... so a little higher ratio of OptiPrep : media would
perfectly match O's silicone oil at 1.405). For OptiPrep's R.I.'s mixed
with aqueous solutions (but not neat),
http://www.axis-shield-density-gradient-media.com/C01.pdf

http://www.axis-shield-density-gradient-media.com/V01.pdf


http://gr5.org/index_of_refraction/


    In order of IOR

Material IOR Comments
Silicone Oil 1.520 Seems easier to buy pyrex rods on ebay than to get
this although it sounds safe, nontoxic (I think?) and I assume you can
mix it with wesson.
Standard Glass 1.512 Used in drinking glasses, windows. Most common
glass. aka soda-lime. ior is much too high to use vegetable oils
Vegetable Oil 1.48 to 1.47 I only like Wesson because it has less color
Pyrex Glass 1.47 to 1.474 aka borosilicate. Ideal for making disappear.
Mineral Oil 1.461 to 1.462 aka baby oil
Quartz Glass 1.4585 Uncommon. Used in cases where you need UV
transparency or very high temperatures.
Water 1.33

more IOR valueshere <http://physics.info/refraction/>andhere.
<http://en.wikipedia.org/wiki/List_of_refractive_indices>


And see wikipedia page
https://en.wikipedia.org/wiki/List_of_refractive_indices



On 4/5/2018 10:49 AM, Etai Sapoznik wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Dear all,
> We are looking to use oil for refractive index matching with BABB. We need large quantities (several tens of mililiters for each run), so oils from Cargille are too expensive. Are there any alternative sources?
> Does anybody have experience with Ethyl cinnamate or Anethole? We would like to know how corrosive such oils are and if an objective would get damaged if we submerge it in such an immersion medium?
> Lastly, we wanted to know if anyone has experience in using glue which is resistant to BABB so that one can permanently glue an optical window to a chamber that would contain BABB?​
>
> Thank you in advance.
>
> Etai Sapoznik

--


George McNamara, PhD
Baltimore, MD 21231
[hidden email]
https://www.linkedin.com/in/georgemcnamara
https://works.bepress.com/gmcnamara/75   (may need to use Microsoft Edge or Firefox, rather than Google Chrome)
http://www.ncbi.nlm.nih.gov/myncbi/browse/collection/44962650
http://confocal.jhu.edu

July 2017 Current Protocols article, open access:
UNIT 4.4 Microscopy and Image Analysis
http://onlinelibrary.wiley.com/doi/10.1002/cphg.42/abstract
supporting materials direct link is
http://onlinelibrary.wiley.com/doi/10.1002/cphg.42/full#hg0404-sec-0023
figures at
http://onlinelibrary.wiley.com/doi/10.1002/cphg.42/figures