Correlative light and electron microscopy (CLEM) the combination of fluorescence microscopy (FM) with high-resolution electron microscopy (EM). Integrated CLEM is a technique that performs both imaging modalities simultaneously in the same instrument without sample transfer. SECOM is an integrated CLEM that is produced and designed by Delmic. This system is being used worldwide for cancer research, marine biology, neuroscience, and cell biology. However, a recent paper published in the Journal of Microscopy demonstrates a novel application for iCLEM in imaging sedimentary organic matter. In this presentation, you can learn how iCLEM was applied to measure organic matter in geological samples. For questions about correlative microscopy and the SECOM, please leave a comment below or visit www.delmic.com and send us a message. We will respond to your questions as soon as possible!

1. Integration without compromise
Imaging sedimentary organic matter with the integrated
correlative light and electron microscope
Geological materials

2. Integrated CLEM for Geology
• Correlative light and electron microscopy (CLEM) is
the combination of fluorescence microscopy
(FM) with scanning electron microscopy (SEM)
• The integrated CLEM techinique can be used to
identify and characterize the organic matter in shale
hydrocarbon reservoirs [1]
• Correlative microscopy is useful to investigate the
organic matter type and thermal regime in which
organic nanoporosity forms [1]
• It helps to reduce the uncertainty when estimating
the undiscovered hydrocarbon resources [1]
From Valentine & Hackley (2016).Correlative imaging was
performed using sample transfer between two separate
microscope systems: Leica DM-4000 for light microscopy and
Hitachi SU-5000 FE-SEM for electron microscopy.

3. Sedimantary Organic Matter: SEM vs. FM
Provides high resolution (nanometer scale)
images. Organic matter visible in dark grey in
Backscattered Electron (BSE) imaging.
*Limitation: Cannot differentiate between
different types of organic matter (e.g. kerogen
versus solid bitumen) [2]
Provides conclusive identification of type of
organic matter [2]
*Limitation: low resolution (~200 nm)
Electron Microscopy (EM) Fluorescence Microscopy (FM)

4. Why use integrated CLEM?
Challenges when using multiple instruments [3]:
• Time-consuming for sample mapping
• Difficulties in field relocation, reorientation
• Sample damage during transfer
Solution: Imaging sedimentary organic matter in shale simultaneously with a fluorescence
microscope and a scanning electron microscope (Integrated CLEM)
• Overcome these limitations
• Obtain high resolution (SEM) and identification of organic matter type (FM)

5. Integrated CLEM – The SECOM
Electron source
& lenses
Sample
Light microscope
objective
Mirror
Vacuum
Dichroic & emission
filters
Camera
Light source
Secondary electron
detector
SECOM - Integrated SEM and Fluorescence Microscope for simultaneous correlative imaging

6. Sample preparation - 1
• Polished rock section glued to glass slide using cyanoacrylate glue
• Section ground to thickness 20-30 µm, sputter coated with gold (~ 4 nm) and mounted in the
SECOM
iCLEM image with 40% FM and 60% EM contrast
*Limitation: Misregistration of fluorescence image
(green arrows) and electron image (red arrows and
red layer margins due to the fact that the section
was too thick

7. Sample preparation - 2
• Polished rock section glued to glass slide using cyanoacrylate glue
• Section ground to thickness 20-30 µm
• Section “wedged” by applying uneven pressure with fingertips to result in one side
being polished to a vanishing edge
• Sample scored and broken for Argon-milling, which removed scratches and made it
even thinner near the vanishing edge
• Section sputter coated with gold (~ 4 nm) and sample mounted as-is in the SECOM

8. Results: Sample preparation - 2
iCLEM image with 50% FM and 50% EM contrast
Red arrows show authigenic micron-
scale carbonate minerals, not visible
in FM
iCLEM image with 100% EM contrast
Solid bitumen (marked) not visible in
SEM, can be identified in FM

9. Results: Sample preparation - 2
Non-fluorescent solid bitumen and
fluorescent amorphous organic
matter (AOM) can be identified here
(30% FM, 70% SEM)
But they are indistinguishable here
(100% SEM)
High resolution features like sub-
micron carbonate identified in EM,
and different types of organic matter
identified in FM

10. Reference
[1] Hackley, P.C. et al (2016). Utilization of integrated correlative light and electron microscopy (iCLEM)
for imaging sedimentary organic matter. Journal of Microscopy. 267: 1–13.
[2] Hackley, P.C. & Cardott, B.J. (2016) Application of organic petrography in North American shale
petroleum systems: a review. Int. J. Coal Geol.163: 8–51.
[3] Timmermans, F.J. & Otto, C. (2015) Contributed review: review of integrated correlative light and
electron microscopy. Rev. Sci. Instrum. 86: 011501.
*All sample images of this presentation are extracted from the publication “Utilization of integrated correlative light and electron
microscopy (iCLEM) for imaging sedimentary organic matter”

11. Integration without compromise
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Address: Kanaalweg 4, 2628 EB,
Delft, The Netherlands
Website: www.delmic.com
Telephone: +31 (0)15 744 01 58
Email: info@delmic.com
Please visit Delmic’s website to learn more
about integrated CLEM.