This is a collection of the material used for the NorMIC lab on image analysis. The google folder contains the data you will need to follow the lab. Moreover, I also provide links to the files in the detailed explanation below. The presentation used during the lab is found in the google slides. If you are completely new to FIJI, and don't know how to install the software please go to the end of this page for some useful links.
Here you can find the presentation in PDF and also the data we will be working on
Day 1, is a practical introduction to bio-image analysis in ImageJ and FIJI. The material for the practical is a list of ImageJ/FIJI examples that illustrate:
-
Images are numbers
- LUTs
- Multidimensional data
-
Basic image analysis pipeline
- Pre-processing: image filters
- Segmentation
- Post-processing: morphological operations
- Quantification
Download a fresh installation of FIJI.
Below you will find direct links to the files, which are in the training material google folder
Here the demo text file
What is bit depth? have a look at the wiki article on grayscale digital images
Not sure how a histogram is built, check this out
Here the demo geryscale tif
Not sure still about what is metadata, here some info from the ImageJ website. Looking for more info on Look Up Tables (LUTs) then go to the Neubias training resources
Here the demo RGB image
Here the demo tif file with multichannel data
Some good reading on what a BioImage Analysis Workflow is can be found here
Here the demo rice image, a classic!
Some extra information on thresholding and filtering is available from Neubias.
If you are having problems with the segmentation, and want to practice the quantification tasks via "Analyze particles" please use this segmented rice image as a catchup
An important step of many post-processing methods is the Watershed algorithm, some info on how this works in FIJI can be found here. Then there is a world of operations we can do to improve our segmentation. Many of these are what we call Morphological operations, check out how to do these in FIJI using MorphoLibJ
Here catchup videos for the workflows:
Please go to the FIJI donwloads website here
Look at this youtube video: https://youtu.be/7aCZV-hp0-4
Look at this youtube video: https://youtu.be/BwJRFkQh5XE
Please post a question in the Image.sc forum: https://forum.image.sc/
- Online and interactive book on "Introduction to Bioimage Analysis" by Pete Bankhead: https://bioimagebook.github.io/README.html
- ImageJ/FIJI learning: https://imagej.net/Learn
- NEUBIAS: http://eubias.org/NEUBIAS/
- Image.sc Forum https://forum.image.sc/
- Bio-Image analysis wiki http://wiki.cmci.info/start
- Bioimage Data Analysis, Editor: Kota Miura https://analyticalscience.wiley.com/do/10.1002/was.00050003
- Bioimage Data Analysis Workflows, Editors: Kota Miura and Nataša Sladoje https://www.springer.com/gp/book/9783030223854
If you missed the lecture then you can have a look at this recording of a live demo I did for the NMI of Sweden:
