1. I would not cut 2 mm quartz tube with diamond knife - 2 mm of the blade will be ruined, pretty expensive exercise.

2. If "soft matter" inside a capillary will not be treated in proper way (google TEM specimen preparation), it is most probable it will not survive cutting.

So, no. You cannot prepare your specimen in this way, unless you embed small pieces of capillary in a resin and cut it with FIB. Why not to remove "soft matter" from the capillary and treat it properly?

TEM requires a very thin section to transmit the electrons. One way would be to embed the piece in epoxy and slice thin sections at a cold temperature to preserve the soft matter. Why do you require TEM and not SEM?

As Alan pointed out SEM is best to work

I would suggest you to use SEM first. The sample size would definitely fits to the device in LCI facility in your instituton. Good luck !!

1. I would not cut 2 mm quartz tube with diamond knife - 2 mm of the blade will be ruined, pretty expensive exercise.

2. If "soft matter" inside a capillary will not be treated in proper way (google TEM specimen preparation), it is most probable it will not survive cutting.

So, no. You cannot prepare your specimen in this way, unless you embed small pieces of capillary in a resin and cut it with FIB. Why not to remove "soft matter" from the capillary and treat it properly?

A really hard nut to crack I guess... you didn't say anything about the sample you expect to demonstrate either with TEM or SEM... Which might help in a decision for either SEM or TEM and what one could propose as an [at least] attempt to prepare (= save, stabilize and conserve) a specimen for further examination... As Vladimir pointed out, it perhaps would be possible to separate the "soft matter"anyhow from the inside surface of the capillary (if it hasn't agglutinated or coagulated yet (e. g. in case of a 'blood filled' 'capillary')... if you try to flush the capillary (e. g. with a kind of usual buffer or Ringer solution, eventually by means of "softly" forced pressure into a suited petridish... and then fixing the sample ['plug'] properly.... ?

It would be very convenient for you to tell us approximately what kind of sample you want to prepare and observe.

Both TEM and SEM have many possibilities today, but as Wladimir and Wolfgang say, the matter of the capillary glass complicates things a lot. Anyway, we all know that in electron microscopy there is almost nothing impossible. If you can tell us a little more about what is the content of the capillary

Thank you all for comment. Sample in capillary is highly concentrated DNA ( ~ 280 mg/ml). I want to take image to know about the conformation. I just came to know that we can take image either by TEM or SEM. Since I dont have that much expertise about theses techniques. I have highly concentrated DNA ( long duplex) inside 0.01mm Thick quartz capillary and want to take image. Cutting the capillary might not be good idea because it may damage the conformation. Is there any way to take take image with out damaging the capillary?

Thanks

If your question is: can I take SEM or TEM image through 0.01 mm thick quartz glass, then the answers is simple: no. EM differs from optical microscopy, where this could be possible. SEM is a surface method, so you'll end up observing the morphology of the quartz capillary. For TEM, it's way too thick, and needs kind a complicated sample preparation.

I agree with Janez.

To observe DNA you need to have it in a grid for TEM or HRTEM.

Try to deposit a fraction of the DNA from the end of the capillary on a grid with carbon film

It is necessary to remove the sample from the capillary. Then you can dissolve it in a buffer solution and drop to a TEM grid for negative staining and/or metal evaporation shadowing. Another way is an AFM. You can deposit the sample to a smooth surface (mica, silicon, graphite, etc.) and scan it with an AFM. Just google "DNA TEM" and "DNA AFM" - there are a lot of articles with detailed protocols of preparation. The best possible way is Cryo-TEM, but there are not so many places in the world where it can be conducted.

In addition, if the capillary is transparent, it is possible to use microspectroscopy technique for estimation of the conformation.

Good luck!

It seems that Dr. Gyawali wants to observe the sample without disturbing too much the position that the particles may have in the interir of the capillary.

That is why I proposed to lightly support the capillary in the TEM grid.