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3: Microscopy

Biology 160 Lab Manual Laboratory 3 Microscopy PDF complete

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Novel 3-D imaging technology makes fluorescence microscopy more efficient

Dr Kevin Tsia (1st from right) and his team developed a new optical imaging technology to make 3D fluorescence microscopy more efficient and less damaging. (From left: Dr Yuxuan Ren, Dr Queenie Lai and Dr Kevin Tsia) Credit: @The University of Hong Kong

Scientists have been using fluorescence microscopy to study the inner workings of biological cells and organisms for decades. However, many of these platforms are often too slow to follow the biological action in 3-D and too damaging to the living biological specimens with strong light illumination.

To address these challenges, a research team led by Dr. Kevin Tsia, Associate Professor of the Department of Electrical and Electronic Engineering and Programme Director of Bachelor of Engineering in Biomedical Engineering of the University of Hong Kong (HKU), developed a new optical imaging technology—coded light-sheet array microscopy (CLAM) - which can perform 3-D imaging at high speed, and is power efficient and gentle enough to preserve living specimens during scanning at a level that is not achieved by existing technologies.

This advanced imaging technology was recently published in Light: Science & Applications. A US patent application has been filed for the innovation.

"CLAM allows 3-D fluorescence imaging at high frame rate comparable to state-of-the-art technology (

10's volumes per second). More importantly, it is much more power efficient, being over 1,000 times gentler than the standard 3-D microscopes widely used in scientific laboratories, which greatly reduces the damage done to living specimens during scanning," explained Dr. Tsia.

Existing 3-D biological microscopy platforms are slow because the entire volume of the specimen has to be sequentially scanned and imaged point-by-point, line-by-line or plane-by-plane. In these platforms, a single 3-D snapshot requires repeated illumination on the specimen. The specimens are often illuminated with thousands to million of times more intensity than that of sunlight. This is likely to damage the specimen itself, thus is not favorable for long-term biological imaging for diverse applications like anatomical science, developmental biology and neuroscience.

Moreover, these platforms often quickly exhaust the limited fluorescence "budget"—a fundamental constraint that fluorescent light can only be generated upon illumination for a limited period before it permanently fades out in a process called "photo-bleaching," which sets a limit to how many image acquisitions can be performed on a sample.

Coded Light-sheet Array Microscopy (CLAM) Credit: @The University of Hong Kong

"Repeated illumination on the specimen not only accelerates photo-bleaching, but also generates excessive fluorescence light that does not eventually form the final image. Hence, the fluorescence 'budget' is largely wasted in these imaging platforms," Dr. Tsia added.

The heart of CLAM is transforming a single laser beam into a high-density array of 'light-sheets' with the use of a pair of parallel mirrors, to spread over a large area of the specimen as fluorescence excitation.

"The image within the entire 3-D volume is captured simultaneously (i.e. parallelized), without the need to scan the specimen point-by-point or line-by-line or plane-by-plane as required by other techniques. Such 3-D parallelization in CLAM leads to a very gentle and efficient 3-D fluorescence imaging without sacrificing sensitivity and speed," as pointed out by Dr. Yuxuan Ren, a postdoctoral researcher on the work. CLAM also outperforms the common 3-D fluorescence imaging methods in reducing the effect of photo-bleaching.

To preserve the image resolution and quality in CLAM, the team turned to Code Division Multiplexing (CDM), an image encoding technique which is widely used in telecommunication for sending multiple signals simultaneously.

"This encoding technique allows us to use a 2-D image sensor to capture and digitally reconstruct all image stacks in 3-D simultaneously. CDM has never been used in 3-D imaging before. We adopted the technology, which became a success," explained by Dr. Queenie Lai, another postdoctoral researcher who developed the system.

As a proof-of-concept demonstration, the team applied CLAM to capture 3-D videos of fast microparticle flow in a microfluidic chip at a volume rate of over 10 volumes per second comparable to state-of-the-art technology.

3D imaging at high speed with CLAM. Credit: The University of Hong Kong

"CLAM has no fundamental limitation in imaging speed. The only constraint is from the speed of the detector employed in the system, i.e. the camera for taking snapshots. As high-speed camera technology continually advances, CLAM can always challenge its limit to attain an even higher speed in scanning," highlighted by Dr. Jianglai Wu, the postdoctoral research who initiated the work.

The team has taken a step further to combine CLAM with HKU LKS Faculty of Medicine's newly developed tissue clearing technology to perform 3-D visualization of mouse glomeruli and intestine blood vasculature in high frame-rate.

"We anticipate that this combined technique can be extended to large-scale 3-D histopathological investigation of archival biological samples, like mapping the cellular organization in brain for neuroscience research." Dr. Tsia said.

"Since CLAM imaging is significantly gentler than all other methods, it uniquely favours long term and continuous 'surveillance' of biological specimen in their living form. This could potentially impact our fundamental understanding in many aspects of cell biology, e.g. to continuously track how an animal embryo develops into its adult form to monitor in real-time how the cells/organisms get infected by bacteria or viruses to see how the cancer cells are killed by drugs, and other challenging tasks unachievable by existing technologies today," Dr. Tsia added.

CLAM can be adapted to many current microscope systems with minimal hardware or software modification. Taking advantage of this, the team is planning to further upgrade the current CLAM system for research in cell biology, animal and plant developmental biology.


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Shibata, M., Uchihashi, T., Ando, T. & Yasuda, R. Long-tip high-speed atomic force microscopy for nanometer-scale imaging in live cells. Sci. Rep. 5, 8724 (2015).

Uchihashi, T., Watanabe, H., Fukuda, S., Shibata, M. & Ando, T. Functional extension of high-speed AFM for wider biological applications. Ultramicroscopy 160, 182–196 (2016).

El-Kirat-Chatel, S. & Dufrene, Y. F. Nanoscale imaging of the Candida — macrophage interaction using correlated fluorescence-atomic force microscopy. ACS Nano 6, 10792–10799 (2012).

Sharma, A., Anderson, K. & Muller, D. J. Actin microridges characterized by laser scanning confocal and atomic force microscopy. FEBS Lett. 579, 2001–2009 (2005).

Schillers, H., Medalsy, I., Hu, S., Slade, A. L. & Shaw, J. E. PeakForce Tapping resolves individual microvilli on living cells. J. Mol. Recognit. 29, 95–101 (2016).

Benoit, M., Gabriel, D., Gerisch, G. & Gaub, H. E. Discrete interactions in cell adhesion measured by single-molecule force spectroscopy. Nat. Cell Biol. 2, 313–317 (2000).

Krieg, M. et al. Tensile forces govern germ-layer organization in zebrafish. Nat. Cell Biol. 10, 429–436 (2008).

Cuerrier, C. M., Gagner, A., Lebel, R., Gobeil, F. Jr & Grandbois, M. Effect of thrombin and bradykinin on endothelial cell mechanical properties monitored through membrane deformation. J. Mol. Recognit. 22, 389–396 (2009).

Pelling, A. E., Veraitch, F. S., Chu, C. P., Mason, C. & Horton, M. A. Mechanical dynamics of single cells during early apoptosis. Cell Motil. Cytoskel. 66, 409–422 (2009).

Ramanathan, S. P. et al. Cdk1-dependent mitotic enrichment of cortical myosin II promotes cell rounding against confinement. Nat. Cell Biol. 17, 148–159 (2015).

Stewart, M. P. et al. Hydrostatic pressure and the actomyosin cortex drive mitotic cell rounding. Nature 469, 226–230 (2011).

Duman, M. et al. Improved localization of cellular membrane receptors using combined fluorescence microscopy and simultaneous topography and recognition imaging. Nanotechnology 21, 115504 (2010).

Lipke, P. N. et al. Strengthening relationships: amyloids create adhesion nanodomains in yeasts. Trends Microbiol. 20, 59–65 (2012).

Alsteens, D. et al. Nanomechanical mapping of first binding steps of a virus to animal cells. Nat. Nanotech. 12, 177–183 (2017). This paper showed that attaching a rabies virus to the AFM stylus allows living animal cells to be imaged with confocal microscopy and AFM, to simultaneously localize virus-binding, and to quantify the virus-binding process and free-energy landscape.

Churnside, A. B. & Perkins, T. T. Ultrastable atomic force microscopy: improved force and positional stability. FEBS Lett. 588, 3621–3630 (2014).

King, G. M., Carter, A. R., Churnside, A. B., Eberle, L. S. & Perkins, T. T. Ultrastable atomic force microscopy: atomic-scale stability and registration in ambient conditions. Nano Lett. 9, 1451–1456 (2009).

Franz, C. M. & Muller, D. J. Analysing focal adhesion structure by AFM. J. Cell Sci. 118, 5315–5323 (2005).

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Microscope Kit for Apologia Biology

Help students get the most out of their microscope labs with this Apologia biology microscope kit! This kit comes with microscope slides and other items for Apologia's Exploring Creation with Biology course. Read More


Help students learn about earth science and biology. Get the most out of their microscope labs with this Apologia Biology Microscope lab kit! This kit comes with microscope slides and other items needed for the microscope portion of Apologia's Exploring Creation with Biology course, 3rd edition.

To make this biology kit and your science experiences more impactful and affordable, we provide an Ascaris (roundworm) slide instead of the more expensive whitefish blastodisc one. Both show animal mitosis, but the Ascaris slide actually shows the stages more clearly!

This Apologia science kit provides the materials for an essential part of Apologia's Biology course. For an even more well-rounded Apologia biology lab experience, pair this kit with the Dissection Kit for Apologia Biology.

If you are ordering this kit, you do not need to order the Apologia Prepared Slide Set in addition. If you are looking for to create your own biology slides, be sure to browse our blank slides before checkout.

If you are looking for materials for Apologia's Exploring Creation with Biology course, 2nd edition simply order this science lab kit along with our Chick Embryo Study Guide.

Important Note:

A microscope is required to do the microscope labs in this Apoligia biology course. Here are two excellent recommendations:

  • We recommend our affordableHome Microscope - a best-seller and a very popular choice for homeschool families! It's sturdy, easy-to-use, features long-life, variable-intensity LED lighting & allows observers to see intricate cell details
  • Apologia recommends the National Optical Advanced Microscope - a more expensive, but also excellent, option

You can also check out our Selecting a Microscope guide for further help and insight when choosing a microscope that best meets your family's needs.


More Information


Apologia Biology Microscope Kit

This kit includes the following items (download the kit order form to order individual or optional items):

Individual slides

  • Ascaris Mitosis
  • Allium (onion) Root Tip
  • Amoeba Proteus
  • Euglena
  • Diatoms (marine)
  • Ficus (dicot) Leaf with Vein
  • Grantia (sponge) Spicules
  • Hydra (budding)
  • Paramecium
  • Planaria (injected)
  • Ranunculus (dicot) Stem
  • Ranunculus (dicot) Root
  • Spirogyra
  • Volvox
  • Zea Mays (monocot) Stem
  • Zea Mays (monocot) Root

Other items

  • Iodine Solution (Lugol's) 30ml
  • Lens Cleaning Paper, 50/pack
  • Methylene Blue, 1%, 15 ml
  • 4 Pipets (medicine droppers)
  • Slide Coverslips, student
  • 12 Plain Glass Slides
  • 12 Concave Slides


My Science Perks is FREE! Just place your order while logged in to your Home Science Tools account and you'll automatically earn up to 6% back when your order ships!

How to Prepare Microscope Slides

This article was co-authored by Bess Ruff, MA. Bess Ruff is a Geography PhD student at Florida State University. She received her MA in Environmental Science and Management from the University of California, Santa Barbara in 2016. She has conducted survey work for marine spatial planning projects in the Caribbean and provided research support as a graduate fellow for the Sustainable Fisheries Group.

There are 7 references cited in this article, which can be found at the bottom of the page.

wikiHow marks an article as reader-approved once it receives enough positive feedback. In this case, 89% of readers who voted found the article helpful, earning it our reader-approved status.

This article has been viewed 52,259 times.

Microscope slides are used to examine single-celled organisms and to look up-close at small plants and organisms. There are two types of prepared slides: dry mounts and wet mounts. Each type of preparation method is used for mounting different types of cells. If you’re wet mounting a particularly pale or translucent specimen, you may need to stain the specimen so it’s visible beneath the microscope.

For dates, locations and anticipated attendance of major national meetings check out the FASEB, Biophysical Society, American Association for Cell Biology, and Microscopy Society of America.

A virtual workshop on Advances in COVID-19 Prevention and Treatment Enabled by Structural Biology Research will be hosted by the Advanced Photon Source at Argonne National Laboratory on May 11 and May 12, 2021.
Broadly, the workshop will present areas where structural biology research, including macromolecular crystallography and cryoelectron microscopy, intersects with in vivo, in vitro, and in silico studies of SARS-CoV-2 and COVID-19. More precisely, the topics will include (a) viral biology, (b) vaccine, therapeutic, and diagnostic antibody studies, and (c) small-molecule drug discovery as it relates to viral proteases and other viral proteins. In addition, as this year’s events emphasize the need for a coordinated, long-term strategy to prevent future pandemics of zoonotic origin, a broader One Health perspective on viral pathogens will be presented.

The exciting list of speakers includes: Pamela Bjorkman, Andrea Carfi, James Davis, Alice Douangamath, Haley Dugan, Yogesh Gupta, Robert Hoffman, Nicholas Hurlburt, Andrzej Joachimiak, Christine Kreuder Johnson, Youngchang Kim, Fang Li, Jonna Mazet, Jason McLellan, Andrew Mesecar, Arvind Ramanathan, Erica Saphire, Karla Satchell, Natalie Strynadka, Drew Weissman, Ian Wilson, and Cheng Zhang.

The workshop is hosted by Michael Becker (GM/[email protected]), Karolina Michalska (SBC-CAT), and Kay Perry (NE-CAT). It is part of the Virtual APS/CNM User's Meeting and will be held from 10AM to

3PM Central Time on May 11 and May 12, 2021. To attend the workshop, register (for free) for the APS User's Meeting and choose WK #9. You must select both sessions, separately, to register for the workshop.

New Microscopy Technique Shows Cells’ 3-D Ultrastructure in New Detail

The method melds the best of super-resolution fluorescence and electron microscopy to show how proteins relate to cells’ fine structure.

Inside a cell, tentacled vesicles shuttle cargo for sorting. Neighboring neurons cling to one another through a web-like interface. DNA rearranges in the nucleus as stem cells differentiate into neurons. And a new microscopy technique shows it all, in exquisite detail.

The technique, called cryo-SR/EM, melds images captured from electron microscopes and super-resolution light microscopes, resulting in brilliant, clear, detailed views of the inside of cells – in 3-D.

For years, scientists have probed the microscopic world inside cells, developing new tools to view these basic units of life. But each tool comes with a tradeoff. Light microscopy makes it simple to identify specific cellular structures by tagging them with easy-to-see fluorescent molecules. With the development of super-resolution (SR) fluorescence microscopy, these structures can be viewed with even greater clarity. But fluorescence can reveal only a few of the more than 10,000 proteins in a cell at a given time, making it difficult to understand how these few relate to everything else. Electron microscopy (EM), on the other hand, reveals all cellular structures in high-resolution pictures – but delineating one feature from all others by EM alone can be difficult because the space inside cells is so crowded.

Combining the two techniques gives scientists a clear picture of how specific cellular features relate to their surroundings, says Harald Hess, a senior group leader at the Howard Hughes Medical Institute’s Janelia Research Campus. “This is a very powerful method.”

Janelia Research Scientist David Hoffman and Senior Scientist Gleb Shtengel spearheaded the project under the leadership of Hess and Janelia senior fellow Eric Betzig, an HHMI Investigator at the University of California, Berkeley. The work is described January 16, 2020, in the journal Science.

First, the scientists freeze cells under high pressure. That halts the cells’ activity quickly and prevents the formation of ice crystals that can damage cells and disrupt the structures being imaged. Next, the researchers place samples in a cryogenic chamber, where they’re imaged in 3-D by super-resolution fluorescence microscopy at temperatures less than ten degrees above absolute zero. Then, they’re removed, embedded in resin, and imaged in a powerful electron microscope developed by the Hess lab. This scope shoots a beam of ions at the cells’ surface, milling away bit by bit while taking pictures of each newly exposed layer. A computer program then stitches the images together into a 3-D reconstruction.

Finally, researchers overlay the 3-D image data from both microscopes. The result: stunning imagery that reveals cells’ inner details with remarkable clarity.

Below, a few examples of this imagery illustrate how scientists are using the technique. “There’s already been a lot of interest,” says Hess. “There are so many more experiments to do — a whole world of cells out there to study.”

The nucleus of a neuron looks dramatically different before (left) and after (right) the cell begins to assume its final adult role. As the cell matures, DNA is repackaged within the nucleus to turn on a new set of genes. These changes are reflected in the different patterns of gray mottling and colored fluorescence inside the two cells. “The technique provided an amazingly detailed snapshot of the state of the nucleus before and after differentiation,” says David Solecki of St. Jude Children’s Research Hospital, who collaborated on the project. Credit: D. Hoffman et al./Science 2020

Developing neurons stick together. This video shows exactly how those cells adhere to each other, revealing Swiss-cheese-like linkages that help young neurons properly migrate to their final destinations in the nervous system. Purple and green super-resolution fluorescence images of adhesion proteins at these linkages correlate with electron microscopy images showing the membrane’s structure in detail. Credit: D. Hoffman et al./Science 2020

Cells are filled with small vesicles ­­– membrane-bound sacks that help cells store proteins, break down cellular garbage, and carry cargo. These many varieties of vesicles are indistinguishable from each other under an electron microscope alone. But with cryo-SR/EM, their distinct features become clear. This clip zooms in on endosomes, which shuttle cargo to different regions within the cell. Credit: D. Hoffman et al./Science 2020

Researchers from outside Janelia can access the technique through Janelia’s Advanced Imaging Center.

New Microscope Captures Detailed 3-D Movies of Cells Deep Within Living Systems

Merging lattice light sheet microscopy with adaptive optics reveals the most detailed picture yet of subcellular dynamics in multicellular organisms.

An immune cell migrates through a zebrafish's inner ear while scooping up particles of sugar (blue) along the way. Credit: T. Liu et al./Science 2018

Our window into the cellular world just got a whole lot clearer.

Physicist Eric Betzig, a group leader at the Howard Hughes Medical Institute’s Janelia Research Campus, and colleagues report the work April 19, 2018, in the journal Science.

Scientists have imaged living cells with microscopes for hundreds of years, but the sharpest views have come from cells isolated on glass slides. The large groups of cells inside whole organisms scramble light like a bagful of marbles, Betzig says. “This raises the nagging doubt that we are not seeing cells in their native state, happily ensconced in the organism in which they evolved.”

Even when viewing cells individually, the microscopes most commonly used to study cellular inner workings are usually too slow to follow the action in 3-D. These microscopes bathe cells with light thousands to millions of times more intense than the desert sun, Betzig says. “This also contributes to our fear that we are not seeing cells in their natural, unstressed form.

“It’s often said that seeing is believing, but when it comes to cell biology, I think the more appropriate question is, ‘When can we believe what we see?’” he adds.

To meet these challenges, Betzig and his team combined two microscopy technologies they first reported in 2014, the same year he shared the Nobel Prize in Chemistry. To unscramble the light from cells buried within organisms, the researchers turned to adaptive optics – the same technology used by astronomers to provide clear views of distant celestial objects through Earth’s turbulent atmosphere. Then, to image the internal choreography of these cells quickly, yet gently, in 3-D, the team used lattice light sheet microscopy. That technology rapidly and repeatedly sweeps an ultra-thin sheet of light through the cell while acquiring a series of 2-D images, building a high-resolution 3-D movie of subcellular dynamics.

The new microscope is essentially three microscopes in one: an adaptive optical system to maintain the thin illumination of a lattice light sheet as it penetrates within an organism, and another adaptive optical system to create distortion-free images when looking down on the illuminated plane from above. By shining a laser through either pathway, the researchers create a bright point of light within the region they wish to image. The distortions in the image of this “guide star” tell the team the nature of the optical aberrations along either pathway. The researchers can correct these distortions by applying equal but opposite distortions to a pixelated light modulator on the excitation side, and a deformable mirror on detection. Over large volumes, the distortions change as the light traverses different tissues. In this case, the team assembles large 3-D images from a series of subvolumes, each with its own independent excitation and detection corrections.

The results offer an electrifying new look at biology, and reveal a bustling metropolis in action at the subcellular level. In one movie from the microscope, a fiery orange immune cell wriggles madly through a zebrafish’s ear while scooping up blue sugar particles along the way. In another, a cancer cell trails sticky appendages as it rolls through a blood vessel and attempts to gain purchase on the vessel wall.

The complexity of the 3-D multicellular environment can be overwhelming, Betzig says, but the clarity of his team’s imaging permits them to computationally “explode” the individual cells in tissue to focus on the dynamics within any particular one, such as the remodeling of internal organelles during cell division.

All this detail is hard to see without adaptive optics, Betzig says. “It’s just too damn fuzzy.” In his view, adaptive optics is one of the most important areas in microscopy research today, and the lattice light sheet microscope, which excels at 3-D live imaging, is the perfect platform to showcase its power. Adaptive optics hasn’t really taken off yet, he says, because the technology has been complicated, expensive, and until now, not clearly worth the effort. But within 10 years, Betzig predicts, biologists everywhere will be on board.

The next big step is making that technology affordable and user-friendly. “Technical demonstrations and publications don’t amount to a hill of beans. The only metric by which a microscope should be judged is how many people use it, and the significance of what they discover with it,” Betzig says.

The current microscope fills a 10-foot-long table. “It’s a bit of a Frankenstein’s monster right now,” says Betzig, who is moving to the University of California, Berkeley, in the fall. His team is working on a next-generation version that should fit on a small desk at a cost within the reach of individual labs. The first such instrument will go to Janelia’s Advanced Imaging Center, where scientists from around the world can apply to use it. Plans that scientists can use to create their own microscopes will also be made freely available. Ultimately, Betzig hopes that the adaptive optical version of the lattice microscope will be commercialized, as was the base lattice instrument before it. That could bring adaptive optics into the mainstream.

“If you really want to understand the cell in vivo, and image it with the quality possible in vitro, this is the price of admission,” he says.

Tsung-Li Liu, Srigokul Upadhyayula, Daniel E. Milkie, Ved Singh, Kai Wang, Ian A. Swinburne, Kishore R. Mosaliganti, Zach M. Collins, Tom W. Hiscock, Jamien Shea, Abraham Q. Kohrman, Taylor N. Medwig, Daphne Dambournet, Ryan Forster, Brian Cunniff, Yuan Ruan, Hanako Yashiro, Steffen Scholpp, Elliot M. Meyerowitz, Dirk Hockemeyer, David G. Drubin, Benjamin L. Martin, David Q. Matus, Minoru Koyama, Sean G. Megason, Tom Kirchhausen, Eric Betzig, “Observing the Cell in Its Native State: Imaging Subcellular Dynamics in Multicellular Organisms.” Science. Published online April 19, 2018.


Join the Microscopy lab and learn about the different types of microscopy to understand the mechanisms behind. You will be trained in light microscopy, transmission electron microscopy and fluorescence microscopy.

Use magnification

In the Microscopy lab, you will be presented with chicken intestinal slides that have been stained with Anilin, Orange G and Fuchsin. Using the 5x magnification, you will identify the villus, and then proceed with higher magnifications to identify smooth muscle, extracellular tissue, epithelial cells, Goblet cells and the nuclei.

Try out the electron microscope

Electron microscopes can be used to visualize objects that are too small to see when using a light microscope—for example the microvilli, mitochondria and the junctions between cells. In the Microscopy lab, you will examine a chicken intestine slide that is specially prepared for a transmission electron microscope. You can zoom in and out to observe different cellular structures.

Learn about fluorescence staining techniques

You will learn about fluorescence staining techniques and how it can be used to visualize specific structures. For example, by staining the DNA with DAPI, you can easily identify a cell’s nucleus. In this part of the lab, you will examine a chicken intestine sample that is infected with a retrovirus and observe how the virus infects the lymphocytes and how it inhibits inflammation. The retrovirus can be further developed as medicine for coeliac disease.

Watch the video: The Inner Life of the Cell (June 2022).


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