I love FIJI. It's capabilities and talented community of developers are incredible. In the name of democratizing imaging software for the masses and generating repeatable, reliable image processing pipelines, I try to use it for the majority of my image processing and analysis needs. But it's taken me a while to get to that point. … Continue reading My Top FIJI Plugins and Resources for Image Processing and Analysis
Blog
FIJI/ImageJ Definitions Quick Reference
Just to help you navigate some of the unfamiliar image analysis lingo you encounter: Image – 2D Array of gray values, with 8bit (0-255 grey values), 16bit (0-65536), or 32bit (6 decimal resolution any number) Stack – Multiple images stacked on top of each other. Usually makes a 3D data set. 3rd dimension = time, … Continue reading FIJI/ImageJ Definitions Quick Reference
Open Source Imaging Tools
Here's a non-exhaustive list of useful opensource imaging tools I use frequently or have come across and found intriguing/potentially useful. FIJI for image processing and analysis. Java based. Can code macros on most popular coding language, as well as imageJ’s own scripting language. I use this all the time. I swear by it. It’s not … Continue reading Open Source Imaging Tools
Learning 3D CAD from Scratch – Resources
3D Printing, CNC, and many methods of prototyping are quickly becoming ubiquitous tools across science and engineering. We have more access to these tools than ever before. But how do you actually make use of them? Personally, I use Autodesk Inventor - one of the major CAD programs available commonly used for parts and assemblies. … Continue reading Learning 3D CAD from Scratch – Resources
[Images] Random Blob
I use a bunch of random stuff to make sure my microscope is working okay. One of those things is chicken fat... weirdly enough. Coherent Raman imaging is really useful for looking at lipids due to it's naturally high 'nonlinear susceptibility' (jargon for how easy you can move electrons around, and thus change it's local … Continue reading [Images] Random Blob
Tips for Staying Active in the Science Community
Staying active in the scientific community decades ago was primarily run through publishers, issuing rebuttals, commentary, opinions and short discussions on different aspects of various studies. Some researchers would get together at niche conferences to discuss progress and every year or two. By today's standards, this seems pretty slow. Today, with the internet current hold … Continue reading Tips for Staying Active in the Science Community
[Images] Optical Brain Imaging
While attempting to process some of my images from last week, I thought I'd share a cool thing I made (with the help of some others). This is a three-image composite that was taken in a live rat brain using multiphoton microscopy. The red image is NADH autofluorescence, a metabolite responsible for cellular ATP production. … Continue reading [Images] Optical Brain Imaging
[Images] Mitral Valve Collagen
These images are from pig mitral valves using Second-Harmonic Generation (SHG) imaging, which highlights collagen fibrils. The mitral valve is responsible for directing blood flow in your heart. Without it, your heart will not be able to pump blood to the rest of your body. Mitral valves are composed largely of collagen and elastin fibrils … Continue reading [Images] Mitral Valve Collagen
[Images] Fixed Brain Slice
This is one of the first biological samples that I got to image with nonlinear Raman imaging. It is a z-stack fly-through of the deeper cortical layers of a fixed brain slice from a rat. The imaging method is Stimulated Raman Scattering (SRS), which uses vibrational contrast that is native to covalent chemical bonds in … Continue reading [Images] Fixed Brain Slice
[Images] MCF10A Human Mammary Cells
One of the things we focus on in our lab is applications of label-free observations for research and clinical diagnosis. This image is of a nonmalignant human mammary cell line as part of a breast cancer project. The left image is endogenous autofluorescence , which provides metabolic information about the cells related to electron donor … Continue reading [Images] MCF10A Human Mammary Cells