Assignments & Instruction documents

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Image Analysis Manuals/Tutorials 2022/Installation Manuals 2022

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

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Additional Papers 2022 Course

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)
3,4 Book Chapter Sampling
7,8 MW Davidson & M. Abramowitz Optical Microscopy
14 NN Fret Imaging, short introduction
14 A. Jain et al. Review paper data clustering

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Microscopy Facilities at Sylvius Laboratory.

The microscope facilities in the Sylvius Laboratory, also referred to as the Microscopy 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 available.
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 .

The address:
Sylvius Laboratory,
Sylviusweg 72
2333 AL Leiden
Phone: +31 71 527 4700 / 5000

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Image Analysis Assignments 2022.

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 D
02 Measurement & Noise DIP-image/Python 28-04-2022
D, I
03 Scalebars & Restauration DIP-Image/Python 11-05-2022
D, I
04 Time-Lapse Microscopy DIP-Image/Python 23-05-2022
D, I
05 Feature Classification DIP-Image/Python ...
D, I
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

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Sample Exams from previous years

Exam Part 1
Exam Part 2

The material to study for the for tests (2022) is given in this [FILE].

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