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μBrews – Microscopy in the Brewery
Welcome to the home of my video series on how to use a microscope in the home or craft brewery. This is a 10-part series, with episodes released every Monday, Wednesday and Friday starting on February 10, 2020. The goal of this video series is to teach brewery microscopy from the ground up. The first five videos in the series concentrate on understanding and properly using your microscope. The final five videos then show a range of microscopy-based assays that are useful methods to employ in your brewery.
Season 1
µBrews Episode 1 – A Brief Tour of a Light Microscope
In this video I will take you on a quick tour of a microbiological light microscope. In this video I will trace the light path to show how your sample …is illuminated and imaged, all while explaining what the different microscope components do, and what they are called.
This is part of a video series on using microscopy in the home or craft brewery. A full list of published episodes can be found on my µBrews YouTube playlist, or on my blog at http://www.suigenerisbrewing.com/index.php/microbrews/
µBrews Episode 1 – A Brief Tour of a Light Microscope
In this video I will take you on a quick tour of a microbiological …
In this video I will take you on a quick tour of a microbiological light microscope. In this video I will trace the light path to show how your sample …is illuminated and imaged, all while explaining what the different microscope components do, and what they are called.
This is part of a video series on using microscopy in the home or craft brewery. A full list of published episodes can be found on my µBrews YouTube playlist, or on my blog at http://www.suigenerisbrewing.com/index.php/microbrews/
µBrews Episode 2 – How Your Microscope Forms an Image
This video explains how your microscope optics form an image, the …
This video explains how your microscope optics form an image, the importance and role of a condenser on a brewery microscope, describes how these components enable microscopy in the brewery, …and provides you some suggestions on what type of optics you need to perform microscopy in the brewery.
This is part of a video series on using microscopy in the home or craft brewery. A full list of published episodes can be found on my µBrews YouTube playlist, or on my blog at http://www.suigenerisbrewing.com/index.php/microbrews/
µBrews Episode 3 – Focusing & Changing Lenses on a Microscope
This video explains how to properly focus on a sample and change the …
This video explains how to properly focus on a sample and change the objective lenses on your microscope to achieve varying levels of magnification. This is a key skill all …microscopics must master, and this video focuses on the best practices for ensuring that you always find your sample without damaging your microscopes objective lenses.
This is part of a video series on using microscopy in the home or craft brewery. A full list of published episodes can be found on my µBrews YouTube playlist, or on my blog at http://www.suigenerisbrewing.com/index.php/microbrews/
µBrews Episode 4 – Use and Care of an Oil Immersion Lens
Oil immersion lenses are a must-have for any brewery hoping to perform …
Oil immersion lenses are a must-have for any brewery hoping to perform microscopy beyond yeast cell counts. However, using an oil lens properly can be a challenge, and incorrect useage …can damage both the oil lens and the other objective lenses on your microscope. This video demonstrates how to properly and safely use an oil immersion lens, and how to protect both the oil and non-oil lenses to ensure your microscope lasts for years.
This is part of a video series on using microscopy in the home or craft brewery. A full list of published episodes can be found on my µBrews YouTube playlist, or on my blog at http://www.suigenerisbrewing.com/index.php/microbrews/
It can be a challenge to form an artefact-free, high contrast image …
It can be a challenge to form an artefact-free, high contrast image which faithfully reproduces the colour of your sample, with a microscope. The most critical step in forming such …an image is properly aligning the condenser of your microscope. This video shows how to align an Abbe-style condenser to produce Kholer illumination – an illumination pattern which limits artefacts and enhances the contrast and colour of your sample.
This video demonstrates this procedure and explains the basic physics achieved by Kholer illumination. A much more detailed description of the goal, physics and outcome of Kholer illumination can be found over at Microcourses: https://www.youtube.com/watch?v=ZRZ9_ov6Fak
This is part of a video series on using microscopy in the home or craft brewery. A full list of published episodes can be found on my µBrews YouTube playlist, or on my blog at http://www.suigenerisbrewing.com/index.php/microbrews/
The simplest and quickest way to look at a yeast sample is using a …
The simplest and quickest way to look at a yeast sample is using a method called a wet mount. In this technique a small amount of a yeast (or other) …sample is placed between a slide and a coverslip, using a narrow thread or hair to create a layer of the sample thin enough to be easily imaged with a microscope. This video provides a step-by-step guide on how to prepare a wet mount, and shows you how to get the best quality images from a sample prepared in this fashion.
Wet mounts differ from other imaging methods in one key aspect – wet mounts keep your sample alive. As such, knowing how to perform a wet mount is critical if you want to perform viability or vitality staining – the topics of Episode 7 of µBrews.
This is part of a video series on using microscopy in the home or craft brewery. A full list of published episodes can be found on my µBrews YouTube playlist, or on my blog at http://www.suigenerisbrewing.com/index.php/microbrews/
A common question in the brewery is whether a yeast pitch is healthy …
A common question in the brewery is whether a yeast pitch is healthy enough to use on brewday. This question can be answered by staining the yeast with dyes that …indicate whether the yeast are alive (viability staining) and which assess the energy stores available to the yeast (vitality staining).
In this video I demonstrate how to perform viability and vitality staining.
Trypan blue is used for viability staining. This is a dye which is excluded from living cells, but which can enter and accumulate in dead cells, thus staining these cells a deep blue. Iodine is used for vitality staining. Iodine stains glycogen – the primary energy store of yeast – a dark brown, allowing a brewer to assess the energy stores available prior to pitching the yeast.
This is part of a video series on using microscopy in the home or craft brewery. A full list of published episodes can be found on my µBrews YouTube playlist, or on my blog at http://www.suigenerisbrewing.com/index.php/microbrews/
µBrews Episode 8 – Performing Cell Counts with a Hemocytometer
Using an adequate pitch rates is critical to ensuring a healthy …
Using an adequate pitch rates is critical to ensuring a healthy fermentation, while for some styles of beer, lower pitch rates are needed to ensure the yeast produce the desired …flavour profile. Ensuring a correct pitch rate requires the ability to accurately determine the concentration of yeast in a yeast sample. This is done by counting yeast, using a specialized slide called a hemocytometer.
In this video I will explain what a hemocytometer is, how it works, demonstrate its correct usage, and walk you through how to calculate the concentration of yeast in a yeast pitch from hemocytometer counts. At the end of the video I will demonstrate how a hemocytometer can be combined with viability staining (trypan blue staining), thus allowing you to quickly and easily determine both the number of living yeast in your sample and your samples overall viability.
This is part of a video series on using microscopy in the home or craft brewery. A full list of published episodes can be found on my µBrews YouTube playlist, or on my blog at http://www.suigenerisbrewing.com/index.php/microbrews/
NOTE: I mis-speak at 4:45, where I state the grid size in the inner region is 0.5 mm – its 0.05 mm[+] Show More
µBrews Episode 9 – Dry Mounts & Staining
Identifying bacteria and smaller yeast in a brewery sample can be …
Identifying bacteria and smaller yeast in a brewery sample can be difficult using wet mounts and conventional widefield microscope illumination. Visualizing these smaller organisms, and identifying intracellular structures in yeast, …requires a more robust and specialized approach to imaging. Specifically, it requires the staining of dried samples with dyes that emphasize cell shape and structure. This approach is required if you wish to track the presence of bacteria during mixed ferments, or identify the presence of smaller yeasts and bacteria in your brewery samples.
In this video I demonstrate the dry mount technique, which is the first step in a range of staining approaches. I then demonstrate the use of three simple and inexpensive stains – safranin o, trypan blue and malachite green – to stain yeast and bacteria on dry mounts.
The stains demonstrated in this video are merely an introduction to the vast array of staining approaches that can be applied to dry mounts. While not covered in this video, more advanced staining methods can be applied to dry mounts, allowing for improved identification of bacteria in your samples (e.g. Gram staining) or identification of specific cellular structures (e.g. India ink to identify bacteria with capsules).
This is part of a video series on using microscopy in the home or craft brewery. A full list of published episodes can be found on my µBrews YouTube playlist, or on my blog at http://www.suigenerisbrewing.com/index.php/microbrews/
µBrews Episode 10 – Digital Imaging, Archiving & Analysis
The ready availability of digital cameras which can be connected to a …
The ready availability of digital cameras which can be connected to a microscope allows brewers to keep a permanent archive of images taken of their brewery samples, and opens the …door to computational analysis of those images. Brewers may want this capacity to monitor changes in the composition or appearance of yeast pitched over successive brews, to track the progress of mixed fermentations, to identify the presence of unexpected organisms in their brewery, to post “cell-fies” to social media, and to perform more rigorous (and potentially even automated) cell counts. In this video I will introduce you to a few options for capturing images from your microscope, and demonstrate how the free image analysis tool FIJI can be used for cell counting.
FIJI is based off of ImageJ, if you don’t want to deal with the complexity of FIJI, you can instead install ImageJ and then manually add the cell counting plugin. ImageJ is available from: https://imagej.nih.gov/ij/
Note: to use the larger phone grip, simply print two of the “Phone_Grip_1of3.stl” files (from thingiverse) and print one of the larger phone grips from my file. When assembling, use the longer phone grip on the bottom of the mount.
This is part of a video series on using microscopy in the home or craft brewery. A full list of published episodes can be found on my µBrews YouTube playlist, or on my blog at http://www.suigenerisbrewing.com/index.php/microbrews/
I’ve had a number of people email me since the release of the µBrews …
I’ve had a number of people email me since the release of the µBrews series, either asking if there were ways to automate cell counting, or asking me whether their …idea to automate cell counting would work.
This video shows a relatively simple way to automatically count cells, using an image of a hemocytometer and built-in features in FIJI. With practice, most users can complete a cell count using this method in less than a minute.
This analysis is also scriptable, using FIJI’s built-in scripting language. In theory, you could reduce your time to perform a cell count to just a few seconds with a well-scripted process.
This is part of a video series on using microscopy in the home or craft brewery. A full list of published episodes can be found on my µBrews YouTube playlist, or on my blog at http://www.suigenerisbrewing.com/index.php/microbrews/
µBrews Bonus Episode – 4 Common Brewery Microscopy Errors & How to Fix Them!
In the 4 years since I published the µBrews series I have had numerous …
In the 4 years since I published the µBrews series I have had numerous brewers contact me with questions about problems they are having with their microscopes. In this video …I distill these down to the four most common problems, and the solutions for each of these issues.
Chapters:
Intro – 0:00
Problem 1 – Unable to focus – 0:24
Problem 2 – Can only focus at low magnification – 4:53
Problem 3 – Cannot Align Condenser – 5:28
Problem 4 – Fuzzy Images – 7:19
Summary – 11:02[+] Show More
