Assignments & Instruction documents



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Image Analysis Manuals/Tutorials 2021/Installation Manuals 2021


Documents for practical part
LINK
The SCIL-image manual
X
The SCIL-image reference manual
X
The DIP-image reference manual
Using the Matlab/DIPLib environment remote
X
Installing Matlab/DIPLib environment local installation
X
Installing Python/DIPLib environment local installation with MacOS or Ubuntu
X
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 2021 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 2021 course.

#
Author
Paper subject (title)
PDF
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 2021.

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.

Assignment
Software
Deadline
PDF / data
01 Acquisition Zeiss, Leica 24-06-2021 A
02 Measurement & Noise DIP-image/Python 26-04-2021
A ,D
03 Scalebars & Restauration DIP-Image/Python 03-05-2021
A ,D
04 Time-Lapse Microscopy DIP-Image/Python 18-05-2021
A ,D
05 Feature Classification DIP-Image/Python ...
31-05-2021
A ,D
06 3D Images & 3D-Processing DIP-image/Huygens/Vaa3D 24-06-2021 A ,D
07 3D Images & 3D-Processing DIP-image/Huygens/Vaa3D 06-07-2021 A ,D

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Sample Exams from previous years


Test
Exam
Answer
Exam Part 1
Exam Part 2

The material to study for the for tests (2021) is given in this [FILE].

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