If you are looking for 100-500µm, there are a lot of µCT scanners that are capable of that. 500µm is already within the scope of medical scanners. But if you are looking at Daphnias, you probably want more like 5 µmish, which is still possible with many desktop systems. I can't help you with a specific machine over in Europe but they can be found in museums and engineering departments (and they might cost something, you you might need to offer co-authorship). As for scanning contrasts, try the linked paper for a start. I've worked with Iodine and PTA and both are good.

http://www.biomedcentral.com/1472-6793/9/11

If you have access to a scanning electronic microscope that would likely suffice for most basic morphological measurements and some more complicated things like geometric morphometric analysis.  You can export the images as TIFFs and SEM would likely be less expensive and more readily available, depending on where you are of course.

I have access for both SEM and micro-CT, but we want to study not only external morphology but also internal. More to that we would like to have full 3D data for didactic uses. Thank you for answer.

If you are looking for 100-500µm, there are a lot of µCT scanners that are capable of that. 500µm is already within the scope of medical scanners. But if you are looking at Daphnias, you probably want more like 5 µmish, which is still possible with many desktop systems. I can't help you with a specific machine over in Europe but they can be found in museums and engineering departments (and they might cost something, you you might need to offer co-authorship). As for scanning contrasts, try the linked paper for a start. I've worked with Iodine and PTA and both are good.

http://www.biomedcentral.com/1472-6793/9/11

Yes, 100-500µm is total size of specimen, so I'm looking for even under 1µm voxel size. Best resolution we can acquire at facility on X-Ray nanotomograph SkyScan 2011. However we are still working out good method of contrasting and fixing microscopic animals. Thanks for article.

Regarding fixing (I presume you mean immobilizing?), there is a slightly complicated protocol called "STABILITY" (see link) that fixes the specimens into position as well as protecting the tissue from shrinking during staining. If you don't need to do that, you could possibly just set a normal agarose gel around your specimens.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084321

Hi,

you can try to apply for beam time at a synchrotron, for example the ESRF in Grenoble - they've a micro anatomy beamline. Anyway, I would suggest SBFSEM ...

... Serial Block Face Scanning Electron Microscopy. It's close to TEM resolution and made for tiny objects, the results are perfectly stacked and you can handle them therefore like CT-data.

Good luck, 

Several MicroCTs have sufficient resolution to scan the samples you are interested in.  You will want a tissue MicroCT such as the Skyscan 1172 or the Scanco 35 or 50.  These systems have a nominal resolution of 5um at the finest image resolution.  This would be sufficient for your larger samples (300um - 500 um).  Sample sizes on the smaller range of 100um will have a lot of blurring with a 5 um spot size.  

You will need to go to something with fraction of a um resolution.  Something like the Xradia UltraXRM-L200 or the Skyscan 2011 or 2211 have resolutions down to 200 nm which would give you sufficient resolution.

As Scanco and SkyScan are in Europe, your best option would be to contact them directly for a list of institutes with there instruments.  You can probably get the companies to run a few sample scans to get an idea how your samples will scan.

Xradia is in the US.  You can contact them also.  It's standard practice to run a sample scan for potential customers.

See the URL links below for additional information.

http://www.scanco.ch

http://www.skyscan.be

You don't have worry about using the Stability method with the hydrogel fixation as described in the PLOS ONE paper outlined above.  That has to do with morphometrically matching the specimens and looking for very subtle differences.   You will find that MicroCT of invertebrates is very dependent on the contrast agents that you use to highlight target structures.  This has to do with the x-ray cross section of tissue being very similar to water and anything that you place the animal in will have that masking its internal structure.  Brian Metschers paper - "MicroCT for comparative morphology: simple staining methods allow high-contrast 3D imaging of diverse non-mineralized animal tissues"  is a great place to get started.  The protocols are robust and straight forward to implement.   I'm attaching the URL link below and a PDF of the paper.

Also see the attached link from the Bruker Skyscan Users Meeting in 2012 scanning Marine organisms.  This should give you some bearing on the utility of microCT for your experiments.  The title of the presentation was "Investigation of contrast enhancing techniques for the application of Micro-CT in marine biodiversity studies" by Faulwetter, Sarah1, Dailianis, Thanos1, Vasileiadou, Aikaterini1, Arvanitidis, Christos from Institute of Marine Biology and Genetics, Hellenic Centre for Marine Research,Thalassocosmos, P.O. Box 2214, 71003 Heraklion, Crete, Greece.

Good luck on your project and finding a suitable microCT.

http://bruker-microct.com/company/UM2012/02.pdf

Article MicroCT for comparative morphology: simple staining methods ...

For samples that small, you might get good results by processing them as for TEM (glut, osmium, resin) and then CT scanning the resin block.Afterwards they can be sectioned if desired.

PTA or iodine stained samples can be embedded (not infiltrated, just immobilized) in agarose in a little tube (I use micropipette tips) for microCT imaging. See

http://cshprotocols.cshlp.org/content/2011/12/pdb.prot067033.full

Two optical (fluorescence) options to consider are SPIM and confocal. Zeiss and Leica make commercial SPIM (light-sheet microscope) systems and might do a test for you. And confocal is worth a try for anything fairly clear and less than half a mm in diameter.

You can use the Skyscan Series Scanner or the Xradia Versa Series Scanner. We use the Xradia Versa 510; it has a minimum resolution/voxel size of .5 um. You will need to preserve your specimen with a formaldehyde base fixatived, e.g. neutral buffered formalin and stain your specimen with either Iodine or PTA. PTA sometimes has trouble penetrating tissues because it is a much larger molecule. I recommend you use iodine. Increase or decrease the concentration of your stain as needed. Then you will need to stabilize your sample in a gel such as agrose or in liquid. Here is a link on how to stain embryos. While bigger than your samples you should be able to adapt the protocol.

http://cshprotocols.cshlp.org/content/2011/12/pdb.prot067033.full.pdf+html

I happen to be one of the beamline scientists at the microtomography station at the ESRF (which Sebastian mentioned above). Feel free to get in touch for a test scan. We can reach for 160 nm voxel size with a point-spread function around 0.5 micron which seems to be well suited for your sample. We just have to consider dose to the sample.