91573 Advanced Microscopy and Imaging
Warning: The information on this page is indicative. The subject outline for a
particular session, location and mode of offering is the authoritative source
of all information about the subject for that offering. Required texts, recommended texts and references in particular are likely to change. Students will be provided with a subject outline once they enrol in the subject.
Subject handbook information prior to 2025 is available in the Archives.
Credit points: 6 cp
Result type: Grade and marks
There are course requisites for this subject. See access conditions.
Anti-requisite(s): 91566 Advanced Microscopy and Imaging AND 91567 Advanced Microscopy and Imaging
Description
This subject provides an in-depth understanding of the theoretical principles of modern microscopy and offers students the opportunity for hands-on use of state-of-the-art research microscopes at UTS. The subject covers theoretical principles of light and fluorescence. Microscopy techniques include bright-field, DIC and phase contrast microscopy. More advanced techniques based on fluorescence labelling, includes confocal microscopy and informative live cell (real-time) imaging. The subject covers background and theory of cutting-edge techniques including super resolution microscopy. The subject reviews all aspects of sample preparation including best practice methods (e.g. use of appropriate controls). Optimised data acquisition for image analysis pipelines is considered. The basic principles of image analysis for quantitative microscopy is covered. Practical sessions provide the opportunity to perform both a fixed and a live cell fluorescence microscopy experiment and allow students to work with their own results data for complex computer analysis and presentation. Results data from the major experiment in the subject are compiled for data analysis, presentation and discussion for the major assessment and are presented in a fashion deemed acceptable at a scientific conference or meeting.
Subject learning objectives (SLOs)
Upon successful completion of this subject students should be able to:
| 1. | Apply the theoretical concepts of microscopy to real world situations |
|---|---|
| 2. | Prepare, fix and stain cells for microscopic analysis and confidently acquire valid data from these instruments |
| 3. | Analyse, present and communicate scientific findings that is of the quality expected for scientific review |
| 4. | Critically evaluate and use information from different sources such as research and review articles, online resources and technical references |
| 5. | Reflect and evaluate the scientific process including individual learning outcomes throughout the subject to identify strengths and future learning opportunities. |
Course intended learning outcomes (CILOs)
This subject also contributes specifically to the development of following course intended learning outcomes:
- Critically appraise and apply advanced knowledge and technical skills to discipline specific projects to inform professional practice in science and medical biotechnology. (1.1)
- Assess, argue for, and conduct independent research and solving complex problems by applying a research methodology to address a research need in a relevant professional context. (2.1)
- Present and communicate complex ideas and justifications using appropriate communication approaches from a variety of methods (oral, written, visual) to communicate with discipline experts, scientists, industry, and the general public. (5.1)
Contribution to the development of graduate attributes
1. Disciplinary knowledge
You will gain disciplinary knowledge in microscopy and its appropriate application in scientific and medical research. This will include an understanding of how optical imaging techniques, available through the many microscopy platforms, can aid in the understanding and knowledge of cellular structures and intracellular processes. You will also develop understanding as to how, in research, the use of microscopy and image data often complements data from other sources, to give a more complete view of intracellular biological processes. Discipline specific knowledge will be assessed in online quizzes (assessment task 1) that will test your ability to understand practical sample preparation notes, image acquisition and image analysis methods that cover general themes in modern microscopy.Through your scientific poster, your depth of knowledge in applying microscopy techniques and data analysis methods to a biological question will be assessed (assessment task 2).
2. Research, inquiry and critical thinking
An Inquiry-oriented approach to research will be gained through problem solving asynchronous learning resources that review equipment and experimental set-up options and through in-person practical classes that employ microscopy to study live and fixed sample material. There will be opportunities for extensive computer image analysis. The practical component of the course will involve acquiring image data to be used in the preparation of a scientiic poster (assessment task 2). The assessment tasks will develop your capacity to present and evaluate microscopy data in various formats whilst simultaneously enhancing your ability to review scientific and technical literature.
5. Communication
You will be assessed on your ability to prepare a scientific poster based on the results generated in the practical sessions (assessment task 2). You will gain experience in both interpreting and discussing your scientific findings in relation to contemporary knowledge by extensively reviewing the current literature. The scientific poster will be presented in a fashion that is considered best practice in the scientific community that publishes microscopy data. You will gain experience in personal reflection and development of your learning journey throught the course (assessment 3).
Teaching and learning strategies
Learning and teaching strategies
At the beginning of this subject, you will be introduced to the content through the online learning space, Canvas. You will have the chance to engage with materials and meet your peers. You will be able to familiarise yourself with the central concepts prior to face-to-face classes, designed to help you further engage in collaboration and critical thinking.
Canvas Pages for asynchronous learning: 5 online modules
Online modules through asynchronous learning are provided as the foundation for your on-campus learning.The lecture series (online and CANVAS pages) have been designed to provide you with the background knowledge necessary for understanding the operation and application of the Microscopy techniques used in Medical Biotechnology. Online readings from discipline-specific reviews are made available to enhance the content that you receive. Asynchronous learning and interactive activities have been developed and tailored towards understanding advanced concepts in Microscopy. They are designed to educate and inspire you to engage in online participation and further discussion with teachers and your peers.
You will gain an in-depth understanding of fluorescence and its uses in microscopy, as well as a grounded understanding of Immunofluorescence microscopy (IFM) and designing IFM experiments. Here, your knowledge will be tested and reinforced by online quizzes. You will learn about digital images, and the quantitative and qualitative data they contain. You will apply these foundation concepts to basic microscopic image analysis with the use of industry-standard software. You will also build on skills in graphing, statistics and referencing. You will have the opportunity for feedback to ensure you have the requisite knowledge to analyze, and present data and data-related statistics for a scientific poster. The online interactive modules will help you through the process of structuring and presenting a scientific poster correctly. You will be challenged to discuss and evaluate experimental design and image analysis in fluorescence microscopy with your peers and through online participation in discussions.
Practicals: A two-day experiment
The practicals give you the opportunity to learn how to prepare and label cells for cellular analysis by optical techniques. Fluorescent reagents, molecular tools and cell treatments will be made available. You will need to understand how the tools, reagents and microscopes work in order to perform the experiment correctly. You will explore the optical and digital parameters of research-grade fluorescence microscopes through experimentation. You will learn to microscopically image cells and the subcellular components which are vitally important for correct cellular function. You will learn about the use of relevant controls that are needed to validate your analysis. You will take images with industry-standard cameras and software. You will conduct a fluorescence microscopy experiment that aims to detect changes in cellular structure in response to a given treatment. The laboratory work is carried out in small groups but will be assessed individually.
Computer class: 1 computer analysis session
In the computer analysis session, which offers active learning of current computer-based analysis techniques, you will learn to analyse microscopy data using industry-standard analysis programs. The data that you analyse will include your own data that you have collected in the practical sessions and more complex data from real-life research projects. This data will be compiled and used to produce figures for the scientifc poster. You will learn how to present, describe and incorporate the data figures into a scientific poster and oral presentation. There will be regular feedback opportunities to ensure your analysis methods, results and poster preparation are of acceptable quality.
Drop-in sessions and online tutorials
Additional drop-in sessions will provide opportunities for further image acquisition using research-grade microscopes to ensure that you obtain high-quality image data (including replicates) of all your treatment conditions and controls. This image data will form the basis of your individual results that require analysis, interpretation and presentation in your own scientific poster. Additional drop-in computer sessions and online tutorials will aid you in the development of your image analysis methods and related skills, including interpretation and presentation of results. Attendance at these drop-in sessions is highly encouraged to maximise your learning outcomes.
Content (topics)
- Light, fluorescence and the compound microscope
- Cell component labelling and immunofluorescence microscopy
- Image analysis
- Understanding and handling images for presentation
- Advanced imaging techniques and applications
- Reviewing literature and scientific writing
- The use of graphs, statistical analysis and data interpretation
- Imaging beyond the diffraction limit
- Power analysis
Assessment
Assessment task 1: Online quizzes
| Intent: | This assessment task contributes to the development of the following graduate attributes:
|
|---|---|
| Objective(s): | This assessment task addresses subject learning objective(s): 1 This assessment task contributes to the development of course intended learning outcome(s): 1.1 |
| Type: | Quiz/test |
| Groupwork: | Individual |
| Weight: | 28% |
| Criteria: | Each quiz may comprise of the following types of questions. Multiple choice questions, multiple answer questions, true/false or questions that need to be matched to answer. The quizzes will be marked for correctness. |
Assessment task 2: Scientific poster
| Intent: | This assessment task contributes to the development of the following graduate attributes: 1. Disciplinary knowledge 2.Research, inqiury and critical thinking 5. Communication |
|---|---|
| Objective(s): | This assessment task addresses subject learning objective(s): 1, 2, 3 and 4 This assessment task contributes to the development of course intended learning outcome(s): 1.1, 2.1 and 5.1 |
| Type: | Presentation |
| Groupwork: | Individual |
| Weight: | 42% |
| Criteria: | Critical analysis of image data with respect to microscopy approaches in research Demonstration of understanding and relevance of microscopy techniques Demonstration of scientific writing skills, poster and oral presentation Ability to correctly reference original sources
|
Assessment task 3: Reflection task
| Intent: | This assessment task contributes to the development of the following graduate attributes: 5. Communication
|
|---|---|
| Objective(s): | This assessment task addresses subject learning objective(s): 5 This assessment task contributes to the development of course intended learning outcome(s): 5.1 |
| Type: | Reflection |
| Groupwork: | Individual |
| Weight: | 30% |
| Criteria: | Reflection Task assesses the following criteria: Clarity - clear and concise description of the situation and concepts that make sense to the reader. Relevance - meaningful reflection of the learning experience that is relevant to the course learning goals. Analysis - critical assessment of learning experience and how this contributed to student understanding of self and course concepts. Interconnections - shows relationships between previous experiences and personal goals relevant to the course. Self-criticism - demonstrates the ability to question their own strengths and challenges relevant to the course, and define new modes of thinking as a result. |
Minimum requirements
In person attendance at all practical and computer sessions is strongly encouraged. The major assessment for this subject is largely based on the content learned and data acquired in both practical and computer classes.
Required texts
There are no specific recommended texts for this subject.
Recommended texts
The web based tutorial sites that are listed below have useful interactive tutorials that complement the lecture and practical program for this subject.
https://www.microscopyu.com
https://myscope.training/