Please report any inconsistencies and/or errors you may encounter in this page.
Documents for practical part
|The SCIL-image manual|
|The SCIL-image reference manual|
|The DIP-image reference manual|
|Using the Matlab/DIPLib environment remote|
|Installing Matlab/DIPLib environment local installation|
|Installing Python/DIPLib environment local installation with MacOS or Ubuntu|
|The Huygens Remote Manager Tutorial|
|Huygens Essential Reference Manual|
|Link to Vaa3D for download Install version (all OS available)|
|Instructions for compiled local install of Vaa3D from the source code|
The papers listed in the table
below provide good additional reading for subjects addresses in
the lectures. These papers are meant for side reading so as to
increase background knowledge.
To be edited for the 2022 course.
Paper subject (title)
|7,8||MW Davidson & M. Abramowitz||Optical Microscopy|
|14||NN||Fret Imaging, short introduction|
|14||A. Jain et al.||Review paper data clustering|
Microscopy Facilities at Sylvius Laboratory.
The microscope facilities in
the Sylvius Laboratory, also referred to as the
Unit will be used to gain experience on image acquisition. At
the Sylvius we are hosted by Gerda Lamers (head microscopy, IBL) and
she will also give practical guidance with the microscopes. Images
are acquired with the confocal microscopes of which there are two
You will obtain a time slot reserved for your team. Please be on time. For your convenience find a map of the location of the Sylvius Laboratory on the Leiden university Campus. Wait at the main entrance where we will pick you up to go to the microscope facilities in the building.
If you have questions, or are unexpectedly prevented at the indicated time, contact the course .
2333 AL Leiden
Phone: +31 71 527 4700 / 5000
Download these assignments and work on them in your team.
In the last column (PDF/data) the "A" links to the pdf of the assignment and the "D" links to the data of the assignment. The deadlines are strict and linked to the submission in Brightspace. Publication of each assignment is announced via BrightSpace and in the News-section of this website. If you experience problems in retrieving these files, please call in assistance from the TA's.
PDF / data
|01 Acquisition||Zeiss, Leica||03-03-2022||
|02 Measurement & Noise||DIP-image/Python||28-04-2022
|03 Scalebars & Restauration||DIP-Image/Python||11-05-2022
|04 Time-Lapse Microscopy||DIP-Image/Python||23-05-2022
|05 Feature Classification||DIP-Image/Python ...
|06 3D Images & 3D-Processing||DIP-image/Huygens/Vaa3D||20-06-2022||D, I|
|07 3D Images & 3D-Processing||DIP-image/Huygens/Vaa3D||20-06-2022||D, I|
|Exam Part 1|
|Exam Part 2|
The material to study for the for tests (2022) is given in this [FILE].