Micro-CT for Soft Tissue (Preclinical) Research

BRUKER SKYSCAN Micro-CTs are advancing the utility of micro-CT scanning of soft tissue imaging. Now more than ever X-ray tomography can be used for imaging structures that were either impossible or difficult to resolve. 

  • Fast scans for excellent tissue separation
  • Simple reorientation, data cropping, and landmarking tools
  • Advanced quantitative analysis for volumetric calculations and tissue structure thickness. 

Gain access to a library of method notes built up over two decades. Extract more information from a micro-CT through the uses of contrast agents and tissue preparation protocols: perfused vasculature for vessel thickness, heavy metal stains (iodine [Lugal’s], phosphotungstic acid (PTA), osmium tetroxide) for tissue differentiation, gold colloids for time-resolved cardiac gating, chemical drying for high resolution imaging, or make use of post-acquisition tools for time-resolved lung and cardiac imaging.

Rat lung, volume rendering

Ex-vivo high resolution lung imaging

High resolution micro-CT provides a 3D solution for measuring the morphometric parameters of lung parenchyma. Through the use of chemical drying of specimens to enhance contrast and stabilize samples,  it is possible to image lung tissue at high resolution, typically around 1μm pixel size or less. At this resolution, the alveolar membranes can be visualized and parameters such as mean cord length and mean linear intercept that are acquired through standard light-microscopy images in 2D can now be calculated in 3D. This provides the obvious advantage that the results are no longer biased by the cross section that is chosen and analyzed. Full 3D integration of the data is now possible. 

Mouse lungs, calculating volume

In-vivo time-resolved lung imaging

Calculate the volume of the lungs in living mice during the different phases (bins) of the breathing cycle through LISTMODE reconstruction function in the NRECON software. Use plug-ins in the custom processing of the CTAN Quantitative analysis program to separate the lung from the surrounding tissue without having to custom draw regions-of-interests. 

Cardiac gating

Cardiac gating

Time resolved imaging doesn’t have to be limited to the lung. By combining SkyScan’s unique LISTMODE acquisition function—collecting very fast images during the acquisition phase and then sorting post-data collection—with the use of perfused contrast agents in vivo, time resolved images of the heart can be acquired and volumetric analysis of blood flow at different stages can be calculated. 


Embryology and developmental biology

Embryology and developmental biology studies require high resolution 3D imaging of embryos, such as of the mouse. However without contrast agent staining, very little soft tissue detail is visible. Here a soft tissue contrast agent, phosphotungstic acid (PTA) is used to stain mouse embryos for micro-CT scanning. The SkyScan micro-CTs achieve high contrast necessary to distinguish anatomical structures all in short acquisition scans required to conduct larger studies.

Related Articles

Micro-CT Applications for Digitizing Biological Specimens

Micro Photonics Inc. provides instruments, laboratory services, training, and support from micro-CT expertsto help research scientists meet their most complex laboratory demands. More information: FREE

What is Micro-CT? An Introduction

Micro-CT is a 3D imaging technique utilizing X-rays to see inside an object, slice by slice. Micro-CT, also called microtomography or micro computed tomography, is similar

Micro-CT Applications in Animal Studies

This is a CT-scanned image of the piranha Catoprion mento. The blue dyed segments inside the skeleton are fish scales eaten by the piranha (also

Not sure about the best instrument for your application?
Do you want to see micro-CT results of your sample?
Our specialists are happy to help.
Not sure about the best instrument for your application?
Do you want to see micro-CT results of your sample?
Our specialists are happy to help.

Coming Soon:

Customer access to tips and instructional videos, method notes, tutorials, application notes, and other content to support your research.


While we are not currently looking to fill a specific position at Micro Photonics, if helping others advance their research is something you are passionate about, then feel free to send us your resume so that we can keep it for further considerations when a position does become available.

Please submit resumes to: info@microphotonics.com

Micro Photonics Inc.
1550 Pond Road, STE 110
Allentown, PA 18104


Due to Covid-19 restrictions, we will not be attending tradeshows in the near future. We are participating in webinars and virtual tradeshows and will post links to those as they are available.

Privacy Policy

What information do we collect? We collect information from you when you register on our site, place an order, subscribe to our newsletter or fill out a form. When ordering or registering on our site, as appropriate, you may be asked to enter your: name, e-mail address, mailing address, phone number or credit card information. You may, however, visit our site anonymously.
What do we use your information for? Any of the information we collect from you may be used in one of the following ways:

; To personalize your experience (your information helps us to better respond to your individual needs).

; To improve customer service (your information helps us to more effectively respond to your customer service requests and support needs).

; To process transactions. Your information, whether public or private, will not be sold, exchanged, transferred, or given to any other company for any reason whatsoever, without your consent, other than for the express purpose of delivering the purchased product or service requested.

; To send periodic emails .The email address you provide for order processing, will only be used to send you information and updates pertaining to your order.Note: If at any time you would like to unsubscribe from receiving future emails, we include detailed unsubscribe instructions at the bottom of each email.

Terms and Conditions

Terms of Service for www.microphotonics.com

Introduction. Welcome to www.microphotonics.com. This website is owned and operated by Micro Photonics Inc. By visiting our website and accessing the information, resources, services, products, and tools we provide, you understand and agree to accept and adhere to the following terms and conditions as stated in this policy (hereafter referred to as ‘User Agreement’), along with the terms and conditions as stated in our Privacy Policy (please refer to the Privacy Policy section below for more information).

This agreement is in effect as of October 25, 2018.

We reserve the right to change this User Agreement from time to time without notice. You acknowledge and agree that it is your responsibility to review this User Agreement periodically to familiarize yourself with any modifications. Your continued use of this site after such modifications will constitute acknowledgment and agreement of the modified terms and conditions.

Responsible Use and Conduct. By visiting our website and accessing the information, resources, services, products, and tools we provide for you, either directly or indirectly (hereafter referred to as ‘Resources’), you agree to use these Resources only for the purposes intended as permitted by (a) the terms of this User Agreement, (b) the terms of any applicable confidentiality, non-disclosure, or other agreement between you and a third party, and (c) applicable laws, regulations and generally accepted online practices or guidelines.

US Partner Form

    Micro-CT Buyers' Guide

      Free Micro-CT Evaluation Scan

      Are you interested in Micro-CT but aren’t sure if it will work for your application?  We would be happy to help you determine if a micro-CT is right for you and guide you to the system that is best suited for your application.  Our micro-CT laboratory has five different Bruker SkyScan Micro-CT systems available for a thorough investigation of your sample.

      Micro-CT results

      Send in a sample and our micro-CT experts will do the rest.  We will select the best instrument, scan the sample, and reconstruct the data.  You will receive a series of cross-sectional images visualizing the interior structure, a 3D model of your results and  a video of your sample with cut-through views. We will also provide our visualization software for enhanced viewing in both 2D and 3D … Explore Within!

      Fill out the form below and will we contact you to arrange the free micro-CT scan.

        Talk to a micro-CT specialist about your application

        Call Now Button