Resources
FLSI Microscopy Resources
Newsletter
Every 1-2 months, Microscopy Facility Director Emery and Lab Manager Sandy will be sending out a newsletter with information on Facility happenings, offerings, and free resources related to microscopy! Please email Emery at ngemery@vt.edu to be added to the mailing list.
View our past newsletters here!
Microscope Comparison
A comparison document of the microscopes offered by FAIM can be found below.
A ~40min video from a Nikon technical rep explaining the confocal microscopes we have, and comparing their applications, can be accessed here.
ImageJ for Beginners course
A free, self-paced, online workshop is available as a Canvas course for Virginia Tech researchers. A Certificate of Completion is available for participants to obtain. An overview of the topics is found below.
To be added to the course, please email flsimicroscopy@vt.edu.
Course length:
Instructional video content, which covers information and demos, totals to 4 hrs and 12 min. If you try all of the exercises, the time to complete the ImageJ for Beginners materials will vary and take up to a work day to complete.
Additional information:
Each module in Canvas will have an optional assignment to upload screenshots or descriptions of questions you have as you work through exercises, and will be regularly checked and responded to.
| Module | Topic(s) |
|---|---|
0 |
Pre-course instructions (download FIJI and Data for the course) and navigation |
1 |
Introduction to images, how we view them, proper and improper image manipulation, and what ImageJ offers |
2 |
FIJI: updating, settings, toolbars and submenus, common options |
3 |
Basic image commands, handling channels, and making figures |
4 |
Using basic shapres to make manual measurements, and using the Record function and ROI Manager |
5 |
Segmentation/Thresholding without and with pre-processing and using the ROI Manager with Analyze Particles |
6 |
Image math for background subtraction, flatfield correction, and applications with segmentation |
7 |
Visualizing 3D images to make presentable figures and videos |
8 |
Basic 3D measurements with 3D Objects Counter and 3D Suite in FIJI |
General Microscopy Resources
Bioimage Publishing Guidelines:
Planning on including microscopy images in a poster or publication, and looking for guidance?
The group QUAREP-LiMi has developed a general image and image analysis publishing checklist as well as a bare minimum imaging parameters requirements checklist.
When including images collected with an instrument from the Facility, please see the Acknowledgements guidelines.
Learning Microscopy Fundamentals:
ThermoFisher's SpectraViewer for comparing fluorescence spectra, seeing what combinations will work, and what lasers will be usable!
Nikon's MicroscopyU: Reading materials and interactive tutoritals
Zeiss's Campus: Reading materials and interactive tutorials
iBiology Microscopy Course Videos: Includes image formation, detection, and specialized techniques
Oxford Instruments Microscopy Training Course: Short videos ranging from background to advanced techniques.
Baylor also has a short introduction to confocal video.
Global BioImaging (GBI) has a free, online mini course on Light Microscopy Technologies.
GBI's MicroTutor offers introductory information and practical knowledge on light microscopy experiments.
OpenCourseWare (MIT) course on Optics for anyone interested in the physics behind ray tracing and image formation.
Free Bioimage Processing/Analysis Tools:
"I have questions that need answers" - visit the image.sc forum!
FIJI (is just ImageJ) - a good workhorse that has a lot of basic tools and plugins. Email flsimicroscopy@vt.edu to be added to the free, self-paced, online ImageJ for Beginners course offered by the Facility!
ZenLite - Zeiss's free version of Zen with limited capabilities. Register to access.
CellProfiler - useful for segmentation pipelines.
QuPath "quantitative pathology" - generally used for tissue slices/whole slide images.
napari - python-based image processing and analysis.