Rue du Bugnon 9, CH-1005, Lausanne, VD, Switzerland
+41 21 692 51 06
CIF Coordinator: jean-yves.chatton@unil.ch

Working From Home as a CIF User

Working From Home as a CIF User

Some of you (and we as well !), while stuck at home due to the COVID-19 outbreak, still need to work on their images. Or maybe you have some spare time you want to dedicate to a topic you’ve never had time to focus on before. Or you just have some practical questions you’d like some answers to. Here’s a collection of useful tips and links you might be interested in in order to continue your work at home, as a CIF user.

If you have other tips or links that might be of some interest to the CIF users, they are welcome too and will be added to this article.

Procedures, Software Available for Free or for Evaluation, and Other Usefuls Tips

General

The CIF Wiki

Let’s start with the basics first. The CIF website has a new section dedicated to all the questions you might ask yourself about imaging, analysis, software, tools and other CIF procedures. It is still starting so you might not find – yet – what you are looking for. If this is the case, do not hesitate to ask us to include your question, your topic, or your suggestions.

The CIF Wiki web page

IT procedures

How to access to your files on the ATHENA server

Through the web

If you need to access your files on our Athena file server, you can use the web interface for this, even without going through the UNIL’s VPN, Pulse Secure or Crypto. See the tutorial on how to access your files with the web interface here:

Mounted as a remote folder (Windows) or a Samba share (MacOS)

You can also access your files directly as a remote folder ONCE you’ve been authenticated through the UNIL’s VPN

Once authenticated, use one of the following procedure to add the ATHENA remote folder if you’re using Windows or MacOS

Online processing

CIF’s Huygens Remote manager (HRM)

The CIF’s deconvolution server is still active and can be used to deconvolve images to enhance resolution and/or signal to noise ratio. If you’re not already a regular user, maybe it’s time to learn the benefits of this service and how to use it. Hop to the dedicated web page to learn more:

If you have trouble using the service or have questions, just ask yannick.krempp@unil.ch

Software download and usage

Software available for extended trials

Miscelleanous

Many microscope brands have free versions of their software. If you’re just looking for a way to view your files, and often export them to a more convenient file format, have a look at the links listed in the article from the Royal Microscopy Society (scroll down for proprietary software with special offers):

Imaris (General)

Imaris has put in place a virtual hub gathering every resources about its software, how to obtain it and how to use it :

Imaris (CIF specific)

Satellite license : In addition to these links we can provide a few Imaris satellite licenses for those who really need access to a complete solution. Please be aware these licenses are available in a very limited quantity and that we cannot fulfill every requests, so please make sure that there is no other solution for your processing needs before asking for this license.

Free Viewer : Many users actually just need a way to see their reconstructed multidimensional dataset in 3D. If this is your case, you can use the free Imaris viewer:

Nikon (CIF specific)

Nikon

Nikon Switzerland has also provided a means to get a trial license valid until June for those using NIS-Elements. If you are interested in this solution, please contact us and provide this information:

  • First name
  • Name
  • Email-adress (with the institutes domain, @bsse.ethz.ch, not @google.ch etc.)
  • Institute
  • Departement
  • PI

For each user and each single licence requested. (More info here)

Zeiss

Zeiss has put in place some extended trials for those working at home:

Leica

Logo

Leica offers on-demand webinars:

Free and Open source software

The CIF has a section dedicated to free software in the downloads area. Have a look !

Learning

CIF’s recommended reading and viewing

This a curated list of some frequently referenced online material and courses that we regularly use in our trainings and workshops. You will also find links to courses from academia and companies in the field of bioimaging. This is a must-read !

As always, if you know of some nice tutorials or free online courses that could benefit other users, please share it with us and we’ll gladly add it to the list.

CIF workshops

You may have time to spare right now, but maybe you couldn’t attend to one of our workshops in the past. There are numerous workshop slides available for download :

If you don’t understand some parts or if you have questions, do not hesitate to ask the respective workshop authors for help or maybe for a one-to-one video session to explain more complex points.

E-learning with LinkedIn Learning for UNIL students/employees

The UNIL offers a free access to LinkedIn Learning (formerly known as Lynda.com) to every UNIL student or employee, as long as they have a UNIL account.

These courses differ from the likes of those available through other online platforms like EDX, Coursera, and Kahn Academy (for those who slept during that particular math course on vectors…) by being focused more on a specific software or tool, often commercial (Office, Adobe suite, etc…) but also some open source packages and even personal development which you won’t find on the other platforms.

Hit the link to get more information on how to access the service :

Here is a list of courses we think you may find useful when working in research and bioimaging :

ADOBE
Photoshop 2020 Essential Training: The Basics
Photoshop 2020 Essential Training: Photography
Photoshop 2020 One-on-One: Fundamentals
Illustrator 2020 Essential Training
Illustrator 2020 One-on-One: Fundamentals
InDesign 2020 Essential Training
Photoshop-Illustrator-InDesign Powercombo for Design
 
GENERAL PROGRAMMING & DEVELOPMENT
Programming Foundations: Fundamentals
Programming Foundations: Algorithms
Programming Foundations: Beyond the Fundamentals
Learning GitHub
GitHub Essential Training
 
PYTHON
Become a Python Developer
Python Essential Training
Introducing Jupyter
Python Data Analysis
Python Statistics Essential Training
OpenCV for Python Developers
Python for Data Visualization
Data Science Foundations: Python Scientific Stack
Essential Math for Machine Learning: Python Edition
Master Python for Data Science
 
R
Learning R
R Statistics Essential Training
Descriptive Healthcare Analytics in R
Master R for Data Science
 
MATLAB
Learning MATLAB
MATLAB 2018 Essential Training
 
STATISTICS
Statistics Foundations: 1
Statistics Foundations: 2
Statistics Foundations: 3
Academic Research Foundations: Quantitative
 
ADVANCED
Advance Your Data Science Skills in Health Sciences
Advance Your Skills in AI and Machine Learning
Advance Your Skills in Deep Learning and Neural Networks
 
AI & MACHINE LEARNING
Artificial Intelligence Foundations: Machine Learning
Become a Machine Learning Specialist
Neural Networks and Convolutional Neural Networks Essential Training
 
BONUS
Remote Working: Setting Yourself and Your Teams Up for Success
Developing a Learning Mindset
Learning Agility
Writing a Research Paper
Technical Writing: Reports

There are obviously many other courses, ranging from Microsoft Office up to very specialized tools like Blender for 3D representation, but also on more personal skills like Project Management, Communication, and even Creativity …

 

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