|
1507 |
|
Cordelières Fabrice P. |
Tutorial |
must understand basic operations in imageJ |
Visualisation |
|
|
1520 |
|
Aguiar Paulo |
Tutorial |
must understand basic operations in imageJ |
Morphological operation |
/neubias-ts2 |
|
1548 |
|
Cordelieres Fabrice P. |
Tutorial |
Early Carreer Investigators without previous experience with image analysis or ImageJ |
Spot detection, Object counting, Object detection |
/neubias-ts2 |
|
1505 |
|
Sampaio Paula |
Tutorial |
must understand basic operations in imageJ |
Image processing |
/neubias-ts2 |
|
1546 |
|
Cardone Giovanni |
Tutorial |
Must understand basics of Matlab as in the TM "Introduction to Matlab" |
Visualisation |
/neubias-ts1 |
|
1420 |
synchrotron |
Tom de Vries, Chong Zhang |
video tutorial |
|
Image segmentation, Phase contrast microscopy, Contrast enhancement, Watershed segmentation |
|
|
1526 |
|
Beth Cimini |
|
|
Machine learning |
|
|
1494 |
|
Jaroslav Icha, Christopher Schmied, Jaydeep Sidhaye, Pavel Tomancak, Stephan Preibisch, Caren Norden |
|
|
|
|
|
55 |
|
|
|
|
|
|
|
1538 |
|
Tisher Christian, Tosi Sebastien |
Tutorial |
ImageJ Macros |
Filament tracing, Visualisation, Fluorescence microscopy, Light-sheet microscopy |
/neubias-ts1 |
|
1847 |
Difference of Gaussian |
Robert Haase |
Workshop material |
|
Cell tracking |
EMBO Course on 3D Developmental Imaging 2022 |
|
1550 |
|
|
Tutorial |
Early Carreer Investigators without previous experience with image analysis or ImageJ |
Montage |
/neubias-ts5 |
|
1521 |
|
Levet Florian |
Tutorial |
Bio Image Analyst |
Super-resolution microscopy |
/neubias-ts3 |
|
1554 |
|
Zaritsky Assaf |
Tutorial |
Bio image analysts |
Collective object tracking |
/neubias-ts7-0 |
|
1372 |
|
Robert Haase |
Tutorial |
|
|
|
|
1854 |
licensing, data sharing, FAIR principles |
|
Workshop material |
|
|
EMBO Workshop on Advanced Methods in Bio-image Analysis, 2021 |
|
1674 |
licensing |
Robert Haase, DFG Cluster of Excellence, "Physics of Life", TU Dresden |
Workshop material |
|
Data sharing |
EMBO Practical Course on Advanced Methods in Bioimage Analysis 2021 |
|
1522 |
|
Tosi Sébastien |
|
|
Image processing |
/neubias-ts3 |
|
1541 |
|
Klemm Anna |
Tutorial |
Early Carreer Investigators without previous experience with image analysis or ImageJ |
Image visualisation |
/neubias-ts4 |
|
1540 |
|
Martins Nuno |
Tutorial |
Early Carreer Investigators without previous experience with image analysis or ImageJ |
Image visualisation |
/neubias-ts2 |
|
70 |
|
|
|
|
|
|
|
6 |
|
|
|
|
|
|
|
1851 |
|
Robert Haase |
Workshop material, video tutorial |
|
Image analysis, Image processing |
NEUBIAS Defragmentation Training School, 2022 |
|
1673 |
|
Robert Haase, DFG Cluster of Excellence, "Physics of Life", TU Dresden |
Workshop material |
|
Interactive segmentation |
Smart Microscopy Workshop at the Center for Cellular imaging at the University … |
|
1517 |
|
|
|
|
|
|
|
1516 |
|
|
|
|
|
|
|
1515 |
|
|
|
|
|
|
|
1513 |
|
|
|
|
|
|
|
1512 |
|
|
|
|
|
|
|
1511 |
|
|
|
|
|
|
|
1510 |
|
|
|
|
|
|
|
1509 |
|
|
|
|
|
|
|
1519 |
|
|
|
|
|
|
|
1518 |
|
|
|
|
|
|
|
1365 |
|
|
|
|
|
|
|
1848 |
Napari, Dimensionality reduction, Python |
Johannes Soltwedel |
|
|
Cell segmentation, Object classification, Object feature extraction |
Trends in Microscopy 2023 |
|
1687 |
|
|
Workshop material |
This course is aimed at scientists working with bioimage data across the life sciences. It is suitable for those involved in creating bioimages or taking their first steps in analysis. The content would also be suitable for those wanting to learn more about the BioImage Archive and gain experience with machine learning approaches for image analysis. The programme will be of particular interest to bio-image analysts with questions relating to the use of ‘big data’ and using the wealth of publically available data curated in the BioImageArchive.
The course should be accessible to members of the bioimaging community and does not require prior experience with machine learning methods or use of the BioImage Archive is necessary, but applicants are encouraged to explore the resources below before starting their application. Applicants should be comfortable with basic programming tasks and have experience working with Python.
Prerequisite reading:
|
Data handling, Cell segmentation, Machine learning, Image analysis |
|
|
1892 |
|
https://metrics-reloaded.dkfz.de/committee |
web |
|
Validation, Image validation, Machine learning |
|
|
1855 |
|
David Legland, Ignacio Arganda-Carreras, Philippe Andrey |
|
|
Morphological operation, Watershed segmentation, Object feature extraction, Texture extraction |
NEUBIAS Academy @Home 2020 |
|
1537 |
|
Miura Kota |
Book Chapter, Tutorial |
|
|
|
|
1677 |
Programming |
Robert Haase, DFG Cluster of Excellence, "Physics of Life", TU Dresden |
Workshop material |
|
Image classification |
|
|
1676 |
|
Robert Haase, DFG Cluster of Excellence, "Physics of Life", TU Dresden |
video tutorial |
|
Image convolution |
|
|
45 |
|
|
|
|
|
|
|
1534 |
|
Horn Martin |
|
|
|
/neubias-ts3 |
|
1581 |
|
Marion Louveaux |
|
|
|
NEUBIAS TS10 (Luxembourg) |
|
1544 |
|
de Castro Aguiar Paulo, Cardone Giovanni, Lindblad Joakim |
Tutorial |
Matlab, for Beginners |
|
/neubias-ts1 |
|
1532 |
|
Beati Igor |
Tutorial |
Bio Image Analysts |
Spot detection |
/neubias-ts3 |
|
1523 |
|
Martins Nuno P. |
|
|
|
/neubias-ts4 |
|
1549 |
|
Cordelieres Fabrice P |
Tutorial |
Early Carreer Investigators without previous experience with image analysis or ImageJ |
|
/neubias-ts5 |
|
1366 |
|
Fabrice Cordeliéres, Ofra Golani |
Tutorial, Workshop material |
must know basics of ImageJ/FIJI |
ImageJ Macros |
NEUBIAS TS1 Facility Staff School - Barcelona 2016 |
|
1503 |
|
Paul-Gilloteaux Perrine |
Tutorial |
|
Bioimage informatics |
/neubias-ts2 |
|
1524 |
|
Arganda-Carreras Ignacio |
Tutorial |
|
Cell segmentation, Morphological operation |
/neubias-ts5 |
|
1497 |
|
Kota Miura |
Tutorial |
none |
Bioimage informatics, Image analysis |
|
|
1858 |
3D image processing |
Thomas Boudier |
video tutorial |
|
Image processing, Image analysis, Object feature extraction, Cell segmentation, Shape features |
NEUBIAS Academy @Home 2020 |
|
1852 |
|
|
|
|
|
HIP Summer School 2021 |
|
1531 |
|
Rueden Curtis |
Tutorial |
Bio Image Analysts |
|
/neubias-ts3 |
|
1373 |
|
Robert Haase, Kouichi C. Nakamura, Jan Eglinger, ImageJ community |
|
|
|
|
|
1883 |
|
|
|
|
|
|
|
1669 |
|
|
Tutorial |
This lesson assumes you have a working knowledge of Python and some previous exposure to the Bash shell. |
Image processing |
|
|
1446 |
|
Arne Seitz, Romain Guiet, Olivier Burri from BIOP EPFL |
|
none. |
Image analysis, Image processing, Light microscopy, High content screening |
|
|
1853 |
|
Robert Haase, Marcelo Leomil Zoccoler |
Workshop material, book |
|
Image analysis, Image processing |
Helmholtz Imaging Incubator Summer Academy – From Zero to Hero |
|
1668 |
|
Jan Eglinger, Stephan Hellfrish, Aliaksandr Halavatyi, Christian Tischer, Toby Hodges, Antonio Politi |
Tutorial |
None if staring from first module, otherwise prerequisites are indicated for each module. |
Image segmentation, Image processing, Image convolution |
|
|
1856 |
|
Anna Klemm |
Workshop material |
To be able to follow the course you need to know basic image analysis:
- concept of “images are a matrix of numbers”
- handling of multi-channel images
- bit-depth
- segmentation by applying an global threshold
- “analyze particles” (connected component analysis)
|
High content screening, Image analysis, Object feature extraction, Cell segmentation |
|
|
1533 |
|
Dufour Axexandre |
|
|
|
/neubias-ts3 |
|
1841 |
|
|
|
|
|
|
|
1551 |
|
Molnar Csaba |
Tutorial |
bio image analysts |
High content screening |
/neubias-ts7-0 |
|
1536 |
|
Golani Ofra, Reinat Nevo |
|
|
Spot detection, Visualisation, Particle tracking, Plotting, Surface rendering |
|
|
1840 |
|
Daniela Vorkel, Robert Haase |
Book Chapter |
|
ImageJ Macros, Image processing |
|
|
1857 |
GPU |
Robert Haase |
video tutorial |
|
Image analysis, Image processing, Cell segmentation, Object feature extraction |
NEUBIAS Academy @Home 2020 |
|
1543 |
|
Klemm Anna |
|
Early Carreer Investigators without previous experience with image analysis or ImageJ |
|
/neubias-ts2 |
|
1542 |
|
Martins Nuno |
Tutorial |
Early Carreer Investigators without previous experience with image analysis or ImageJ |
|
/neubias-ts2 |
|
1506 |
|
Sampaio Paula |
Tutorial |
must understand basic operations in imageJ |
Image analysis |
|
|
1850 |
OME-NGFF, OME-Zarr |
Joel Lüthi, Gustavo de Medeiros, Lucas Pelkmans, Prisca Liberali |
Workshop material |
|
High content screening, Image analysis |
|
|
1502 |
|
Cardone Giovanni, de Castro Paulo, Lindblad Joakim |
Tutorial |
|
Object tracking, Particle tracking |
|
|
1501 |
|
Miura Kota, Cardone Giovanni |
Tutorial |
|
Object tracking, Particle tracking |
|
|
1530 |
|
Tinevez Jean-Yves |
|
Bio Image Analysts |
|
/neubias-ts3 |
|
1580 |
|
RASTI Pejman , ROUSSEAU David |
video tutorial |
Coding notions |
Machine learning, Classification |
|
|
1528 |
|
Cordelières Fabrice P. |
|
Bio Image Analysts |
Colocalisation analysis, Object-based colocalisation, Pixel-based colocalisation |
/neubias-ts7-0 |
|
1654 |
High content single cell phenotypic profiling, Deep learning in microscopy, Public data repositories, data harmonization, integration and fusion, Data-modeling of live cell imaging |
Assaf Zaritsky |
|
No prior biological knowledge is required; all background will be covered in the lectures. Some background in mathematics and programming is required. Prior knowledge in machine learning and/or computer vision is highly recommended, but not necessary. |
Bioimage informatics, Machine learning |
|
|
1675 |
|
Robert Haase, DFG Cluster of Excellence, "Physics of Life", TU Dresden |
Workshop material |
|
ImageJ Macros |
Max Planck BioImaging Core Unit Network - Advanced ImageJ Macro Course, 2021 |
|
1504 |
|
Tisher Christian |
Tutorial |
Early Carreer Investigators without previous experience with image analysis or ImageJ |
Contrast enhancement, Conversion |
/neubias-ts2 |
|
1525 |
|
Karhohs Kyle |
Tutorial |
no need for programmation |
Cell segmentation, Machine learning |
|
|
1535 |
|
Wahlby Carolina |
Tutorial |
None |
Cell segmentation, Cell tracking, Spot detection |
/neubias-ts2 |
|
1842 |
|
Estibaliz Gómez-de-Mariscal |
|
|
|
|
|
1839 |
drosophila, fruit fly, cell migration |
|
book |
|
Image analysis, Machine learning, Data handling, Plotting, Python, ImageJ Macros |
|
|
1643 |
protocols, Icy, automation, reproducibility |
Marion Louveaux |
video tutorial |
Basic image analysis concepts.
Target audience
Early Careers: Ideally suited. Learn how to make reproducible automated bioimage analysis workflows even without programming knowledge
Bioimage Analysts / Facility Staff: Very useful for teaching purposes and if you need to quickly deliver modifiable, reusable workflows to non-programming user
|
|
Recording of the webinar |
|
1529 |
|
Jug Florian, Pietzsch Tobias |
|
|
Visualisation, Data handling |
/neubias-ts7-0 |
|
1500 |
|
Guiet Romain |
|
must know basics of ImageJ/FIJI |
|
/neubias-ts1 |
|
1498 |
|
Guiet Romain, Tosi Sébastien |
Tutorial |
must know basics of ImageJ/FIJI |
Image processing |
/neubias-ts1 |
|
1499 |
|
Tosi Sébastien |
Tutorial |
must know basics of ImageJ/FIJI |
Image processing |
Event |
|
1539 |
|
Helfrich Stefan |
Tutorial |
|
Montage |
/neubias-ts5 |
|
1508 |
|
Cordelières Fabrice P. |
Tutorial |
must understand basic operations in imageJ |
Image visualisation |
|
|
1547 |
|
Miura Kota, Pengo Thomas, Noerrelykke Simon |
Tutorial |
Must understand basics of Matlab as in the Training Material "Introduction to Matlab" |
Particle tracking |
/neubias-ts1 |
|
1552 |
|
Urbancic Vasja, Butler Richard |
Tutorial |
Bio image analysts |
Filament tracing, Isolated object tracking |
/neubias-ts7-0 |
|
1451 |
|
Fabrice Cordelières, Chong Zhang |
|
ImageJ macro knowledge |
Colocalisation analysis, Object-based colocalisation |
/neubias-ts1 |
|
1545 |
|
de Castro Aguiar Paulo, Cardone Giovanni, Lindblad Joakim |
Tutorial |
Must understand basics of Matlab as in the TM "Introduction to Matlab" |
Image segmentation |
/neubias-ts1 |