View source for Microtomography (microCT)

== Statement of Purpose ==
This page will provide an overview of the utility for microtomography in a museum setting, considerations for specimens and considerations for destructive sampling, and resources for further information.

==Introduction==

Micro-CT is ideal for imaging hard, calcified structures such as bone, but the low X-ray absorption of low density non-mineralised tissues means that samples must be stained if soft tissues are to be imaged. (Hall et. al., 2015)

==Keywords==
microCT, MicroCT, microtomography, x-ray, micro-CT, museum specimens, 3D visualisation, virtual specimens

==Methods==
Considerations for DNA and damage to specimen tissue
Iodine stains have been shown to inhibit PCR (Marin, et al., 2000; Auinger, et al., 2008) and the staining and rinsing process (soaking the specimen in stain solution at room temperature for hours/days, then washing post-scan) may leave DNA vulnerable to decay by hydrolysis.

{| class="wikitable" style="margin:auto"
|+ Common Contrast Staining Methods Adapted from Metscher (2009)
|-
! Stain !! Stoc Solution !! Staining Procedure
|-
| PTA || 1% (w/v) phosphotungstic acid in water || Mix 30 ml 1% PTA solution + 70 ml absolute ethanol to make 0.3% PTA in 70% ethanol. Keeps indefinitely.
Take samples to 70% ethanol.
Stain overnight or longer.
Change to 70% ethanol. Staining is stable for months.
Scan samples in 70% – 100% ethanol
|-
| IKI || 1% iodine metal (I2) + 2% potassium iodide (KI) in water || 
Dilute to 10% in water just before use.
Rinse samples in water.
Stain overnight.
Wash in water.
Can be scanned in water or dehydrated to alcohol.
|-
| I2E, I2M  || 1% iodine metal (I2) dissolved in 100% ethanol (I2E) or methanol (I2M) || Use at full concentration or dilute in absolute alcohol.
Take samples to 100% alcohol.
Stain overnight or longer.
Wash in alcohol.
Stain does not need to be completely washed out before scanning.
|-
| Osmium tetroxide || standard EM post-fixation || 


Same as routine EM processing.
Osmium-stained samples can be scanned in resin blocks, with some loss of contrast.
|}















Dissemination of results
Museum policy often requires CT scans be deposited in a publically available domain, wherein the raw data files can be downloaded. Morphosource, an online tool to find, view and download 3D data from the world's natural history collections is bridging this gap in deliverable dataset for the museum community. 
https://www.morphosource.org/?locale=en

==Contributors==


===Equipment===

[https://lp.microphotonics.com/skyscan-1172-product-landing-page/?gclid=Cj0KCQjwmtGjBhDhARIsAEqfDEdQ2ZhqlD5N1igzNm4w2m8xpX35QlCkstbu98qj-jlzqXxbVQ28-UoaAmQ9EALw_wcB|Skyscan%201172%20micro-CT Bruker SkyScan 1172]

[https://www.perkinelmer.com/product/quantum-gx2-instrument-cls149276 Quantum GX2 microCT Imaging System]

[https://www.perkinelmer.com/product/ivis-instrument-spectrum-ct-120v-128201 IVIS SpectrumCT In Vivo Imaging System]

===File Formats===


==Novel Uses==
Microtomography, beyond morphometric analysis, can be used for novel types of specimen exploration as well. In a paper by Sulikowska-Drozd titled: Micro-CT screening of old shell collections helps to understand the distribution of viviparity in the highly diversified clausiliid clade of land snails, microCT was used to determine brooding strategy by scanning ethanol preserved and dry museum specimens. 


==References==
<references/>

Auinger, B., M., et al. 2008. Improved methodology for  identification of Protists and microalgae from  plankton samples preserved in Lugol’s iodine solution: combining microscopic analysis with  Single-cell PCR, Applied Environmental Microbiology. 74(8). pp.2505. 

Hall, A., Sherlock, E., & Sykes, D. (2015). Does micro-CT scanning damage DNA in museum specimens?.

Marin, I., et al. 2000. Preparation of DNA Suitable for  PCR Amplification from Fresh or Fixed Single Dinoflagellate Cells. BioTechniques. 30. pp.88-93 

Metscher B. D. (2009). MicroCT for comparative morphology: simple staining methods allow high-contrast 3D imaging of diverse non-mineralized animal tissues. BMC physiology, 9, 11. https://doi.org/10.1186/1472-6793-9-11

Sulikowska-Drozd, A., Duda, P. & Janiszewska, K. Micro-CT screening of old shell collections helps to understand the distribution of viviparity in the highly diversified clausiliid clade of land snails. Sci Rep 10, 60 (2020). https://doi.org/10.1038/s41598-019-56674-7

[[Category:Desired BP Content]][[Category:Digitization and Imaging]]