MIAP Care Workshop at FMI

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The goal of this workshop is to teach and train participants in Content-aware image restoration (CARE) in fluorescence microscopy (see also: https://www.nature.com/articles/s41592-018-0216-7). After this workshop the participants:

  • are able to identify potential use-cases for CARE
  • are able to set-up a python environment to run CARE
  • are able to set-up a training dataset
  • are able to train a model
  • are able to run a model on new data
  • are able to test the validity of a model
  • are aware of potential mistakes



09:00 – 10:00 Setting up the environment

10:00 – 10:30 Coffee break

10:30 – 11:00 Machine learning basics (*)

11:00 – 11:45 Key note by Florian Jug (*)

11:45 – 12:45 Lunch break

12:45 – 18:00 Tutorial / hands-on


Participants are encouraged to bring their own data. In order to make sure that the data is feasible, a sample can be reviewed by Markus Rempfler/Florian Jug before the workshop.

(*) The seminar takes place from 10:30 – 11:45 and includes both, the machine learning basics and the key note by Florian Jug. 


Registration information:

The registration is for free.

There are only 12 spots available for the tutorial / hands-on session in the afternoon. Participants are selected based on their their letter of motivation in case the organizers receive more than 12 applications.
It is also possible to only register for the seminar part in the morning, which is not subject to this limitation.

Participants of the tutorial are expected to have basic knowledge of the programming language Python.

Please note: There is no catering during lunch time; food options around FMI will be pointed out.


Friedrich Miescher Institute for Biomedical Research (FMI)
Rooms 5.30 and 5.39
Maulbeerstrasse 66
4058 Basel


Tobias Wernet
e-mail: tobias.wernet@zbsa.uni-freiburg.de

Sibylle Bartsch
e-mail: sibylle.bartsch@zbsa.uni-freiburg.de


Friedrich Miescher Institute (FMI)

Markus Rempfler
e-mail: markus.rempfler@fmi.ch

Workshop Details

November 12th 2019