The Integrated Microscopy Core: Revolutionizing Scientific Discovery

The ability to microscopically visualize the tiniest of molecules provides the backbone of basic medical research. The microscopy resources at Baylor College of Medicine, however, are anything but basic. spoke with Michael Mancini, Ph.D., director of BCM’s Integrated Microscopy Core, about how high throughput automation and other advances in microscopic platforms are revolutionizing scientific discovery and hastening research in the areas of drug development and pathology.

What capabilities and resources can investigators find in the Integrated Microscopy Core?

One of the great things about our core is that molecular biology and biochemistry can be integrated into imaging; that is what a modern microscopy lab can do. We have light and electron microscopes, spectral confocal microscopes, deconvolution microscopes, and high throughput microscopes as our main platforms. In addition, exciting new microscopes, including a novel “low-mag/high-resolution” prototype, just arrived.

Our microscopes help investigators answer basic scientific questions. Investigators bring in cell or tissue samples in order to image basic histology and especially to define the levels and localization of particular molecules; the only way to do this is through imaging. There are chemical approaches that can be complementary tools, but being able to identify the location of a molecule using good probes and reagents is fundamental to a wide range of basic sciences and applies to drug screening, experimental therapeutics, et cetera.

Our more advanced microscopes—the deconvolution and the confocal—offer better image resolution and localization. The confocal microscope is an effective tool that allows us to see through thicker tissue samples and to visualize a broader spectrum of fluorochromes using a spectral detector. The deconvolution microscope has arguably better image resolution, but it is not effective for examining thicker specimens. These two platforms get the most use in our lab.

The best instrument for image resolution is an electron microscope. Ours requires specialized processing of tissue samples with an ultramicrotome to create ultrathin slices. Using these ultrathin samples allows visualization of structures at very high resolution. While it provides the greatest image resolution, an electron microscope is unfortunately extremely slow. So, there is a trade-off between sensitivity and speed when using this instrument.

We also have automated high throughput microscopes that allow us to examine multiple samples in 96- or 384-well plates and a setup for taking many thousands of photographs of those samples overnight. Research involving systems biology, drug screening, and cell pathway analysis requires well-organized experiments using the multiwell formats. The high throughput instrumentation can process many 384-well plates using microfluidics robots controlled by custom programming.

We provide not only the instrumentation but also design and develop an appropriate assay to achieve project goals. We help investigators identify the best platform to support their needs and determine the most efficient way to help them get answers to their research questions. Investigators receive the necessary consultation and training so that they themselves can operate the instruments.

What sets Baylor's Integrated Microscopy Core apart from similar labs at other academic institutions?

Most institutions have basic microscopy cores, but what sets us apart is a strong set of automated platforms and access to new technologies through various corporate partners. One of our instruments is a fully automated live-cell high throughput microscope that is remarkably fast. Ten years ago, very few institutions had a full suite of automated high throughput microscopes. Through my association for the past decade with the Gulf Coast Consortium for Chemical Genomics, we have helped to develop a robust high throughput drug-screening platform, running dozens of projects per year. The advantage of high throughput microscopy, as the name implies, is speed. With these systems, we no longer have to sit for hours at a time examining slides one by one. Instead, having the microtiter plate allows us to set up huge experiments. The ability to do that has revolutionized the field of cell biology.

Do most investigators already know how to use the technology and about how it can support their research goals?

Most investigators know what to do to satisfy their basic needs, but many are surprised to learn the extent of what is possible with certain microscopes and various labeling approaches. We train investigators on the proper use of all our equipment and discuss the appropriate means for processing their samples. We also determine the type of workflow they need to prepare their samples. The common samples are labeled with a fluorescent dye and can be imaged on many different microscopes with different degrees of sensitivity and resolution. So, it is imperative that we have detailed discussions with investigators about what they want to accomplish. The Core is best used when there is full dialog with investigators so we can understand the research question they are trying to answer. We then ask our own series of questions to problem solve, define the positive and negative controls, assess the investigator’s expectations and timeline, and determine if we can meet his or her needs.

What types of projects can the Integrated Microscopy Core support?

We have low-, medium-, and high-resolution instruments to accommodate all types of research. Many investigators bring in a paraffin-embedded section that has been simply stained with hematoxylin and eosin. They learn how to use a basic light microscope, take a color picture, and leave with their images on a thumb drive. If investigators lack experience, we offer tutorials on how to perform basic antibody labeling and staining. We have been increasingly doing so in the past year with new fluorescence in situ hybridization approaches, which are used to identify the location of RNA molecules. One researcher came in having trouble visualizing the details of the telomeres at the ends of the chromosomes she was evaluating. After briefly training on our deconvolution microscope, she was able to use it to gather the data she needed—which confirmed her hypothesis—and wrote a rebuttal paper that was ultimately published in Cell.

In terms of complexity, our group used automated high throughput microscopy to conduct an RNAi-knockdown screen of ~300 samples to interrogate mechanisms of estrogen receptor activity. We successfully measured multiple mechanistic steps simultaneously, showing how transcription occurs—all on a cell-by-cell basis rather than the usual individual experiments on large populations of cells that can only deliver ‘average’ results per cell, missing important new attention being paid to cellular heterogeneity, even in common cell lines that can be surprisingly diverse in terms of mRNA or protein expression. The integration of all the simultaneously collected mechanistic data provides an excellent systems-level view of the biology.

Are there any new technologies on the horizon that investigators can expect to see in your lab?

Typically, high magnification is needed to achieve high-resolution images of microscopic organisms. We are working on a new platform that has low (20´) magnification but with the same image resolution as high (100´) magnification without the need for oil immersion lenses. The downside of achieving high resolution has always been a limited visual field—we could see only five cells but we could see them perfectly. This new platform allows us to visualize thousands of cells at the same resolution as a handful, so the speed at which we analyze cells is going to change tremendously. We will get the same data taking one low-magnification picture as we would taking 10 high-magnification pictures. We will be combining the new optical platform with multiplexing of proteins and RNA. It is truly amazing.

Starting out as a cell biologist, you have witnessed major changes in the field of microscopy. What advances do you think have had the greatest impact on research?

High throughput platforms are changing everything. The fact that I just described a new platform that can achieve high-resolution images with a low-magnification lens—who would have thought that would be possible? The opportunities are endless, and as more molecular biology research is rendered to a cell-by-cell analysis, it will be absolutely essential in helping researchers answer questions.

One of the interesting discoveries made in my own lab is the differences that we observe between cells and our ability to interrogate these differences more specifically. Any investigator can scrape a dish of HeLa cells and look for three different proteins biochemically, and there the immunoreactive bands are on a gel. We did that very experiment—looking for three different proteins on a cell-by-cell basis—and we were blown away because the heterogeneity is shocking. No one was paying attention because no one realized the extent of the heterogeneity. Anyway, there wasn’t much we could have done if we had wanted to. Now that it’s possible to interrogate samples on a cell-by-cell basis, we can conduct massive experiments that were once too painstaking to do. I have no doubt that molecular biology research will only continue to grow faster in pace and greater in depth.

Investigators interested in using the Integrated Microscopy Core lab can learn more on the Baylor College of Medicine iLabs Web site at

VIICTR Member Organizations
  • Baylor College of Medicine
  • Texas Children's Hospital
  • MD Anderson Cancer Center
  • Michael E. DeBakey VA Medical Center
  • Ben Taub Hospital
  • University of Houston College of Pharmacy
  • Gulf Coast Consortia