Resources for the life scientist

You will find here scripts, documents, code snippets and more than can be used to build larger applications. This is a work in progress, and if you find bugs or errors don’t hesitate to notify me !

Resources for learning and working with bio-image processing and analysis

1. Basic

1.1. Image Analysis Notions for the Microscopist

Basic notions and concepts like digital images, DPI, scale, interpolation, filtering, and much more using various media to illustrate them: macros, notebooks, PDFs…

Click here to access the repository

2. Advanced

This section is adressed to scientists who already have some programming notions. You will find more advanced topics like python scripting, machine learning, automation using various tools.

2.1. Python and Microscopy

Collection of Jupyter notebooks. Inspired by Python for Microscopists Youtube channel, by Dr Sreenivas B. adapted for the format, but it also contains scripts of my own, and maybe other external additions in the future.

Click here to access the repository

3. Fiji

Fiji scripts and ImageJ macros. Some simple applications, and tools meant to be used as building blocks for more complex projects.

[Work in Progress]

4. Other

5. About me

I work as technical manager and imaging expert at the Cellular Imaging Facility, Lausanne, Switzerland. My focus is on helping researchers to be able to analyze the data they acquire on our instruments. If you’re curious about the facility, head to the CIF website, that I’m also webmastering.

6. Contact

If you wish to contact me directly, here’s my info:

	Yannick Krempp
Position	CIF technical manager and IT specialist
Affiliation	Cellular Imaging Facility
Adress	Rue du Bugnon 9, CH-1005, Lausanne
Office	212
Phone	+41 21 692 52 90
Email	yannick.krempp@unil.ch
Web	https://cif.unil.ch
LinkedIn	https://www.linkedin.com/in/yannick-krempp/

7. Citing

TBD