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EPFLx: IPA4LSx Image Processing and Analysis for Life Scientists

Forum

Questions, discussions and interaction with course instructors happen on the IPA4LS Discourse Forum, hosted by EPFL. The forum uses your edX credentials to authenticate you automatically.

Imporant note: The link above will not work if you are logging in for the first time. Use the button at the bottom of the "Description and Outline" Subsection in each Week to access it. 

Bibliography

Links

  • FIJI : Fiji Is Just ImageJ
  • image.sc Forum 
  • NEUBIAS : Network of European BioImage Analysts 
  • BISE : Bioimage Informatics Search Engine
  • BIOP : BioImaging and Optics Platform

Downloading Sample Images :

HeLa cells , nuclear stainings.

Week-03 images 

Week-04 images

Week-05 images 

Week-06 images : No new images during week 6

Week-07 images

Downloading Sample Macros :

Throughout the course, you will find links to download ImageJ Macro code that highlights aspects of the videos or exercises you've just followed. All of the code is commented, so we encourage you to read through it and understand how it is performing the actions you see. They are meant as interactive educational scripts, which could serve as a base for your image processing and analysis needs.

You can choose between (at least) three ways to get the files 

A- Save the target as a ".ijm" file
    1. Right-click on the file link
    2. Use "Save as ..."
    3. You should get a file save dialog offering you to save the file to your folder of choice, with extension '.ijm'
B- Copy the raw text from the link to FIJI
    1. Click on the link
    2. A new tab should open and show you the code in plain text
    3. Copy the text
    4. In Fiji, open the script editor using Plugins>New Macro...
    5. Paste the text into the script editor
C- From our GitHub Repository  :

You can either:
Download as a Zip file (You'll need to download the Zip file again if there were updates)
or
Clone (you will have to update the folder each week, as new files may be added or updated)

Help on "cloning a repository", can be found on the help.github page.
It can be done using a command terminal but also using GitHub Desktop.