Dear participants,
Please provide us with your feedback, so we can learn and improve ourselves: feedback-form
kind regards,
BIF-team
Dear all,
The BioImaging Facility team organizes an image analysis workshop on June 13 and 14, 2019:
With this workshop we aim to raise awareness to think about your analysis before you acquire data; introduce you to some concepts of image analysis and flash the main available tools that we offer from the BioImaging Facility.
- Our image analysis website: https://iof.pages.ist.ac.at/bif-equipment/image-analysis/
- Available software: https://iof.pages.ist.ac.at/analysis-software/
- Workstations: https://iof.pages.ist.ac.at/bif-equipment/bio-image-analysis-software/
We also provide the opportunity to sign up for a 1 hour Q&A session on the workstation on June 14th for some initial troubleshooting. Please find the putative schedule further below.
- lectures only: a brief email would suffice (just to make sure that we have space)
- ImageJ/FIJI macro-hands on: bring your own laptop and make sure to have FIJI installed! link
- workstation Q&A: please indicate shortly what you would like to do – email
SCHEDULE:
June 13, 2019
- lectures (Foyer seminar room Ground floor / Office Bldg West)
09.00-09.30 – Intro: workshop aims and resources at IST Austria (GaKr)
09.30-10:25 – What is a digital image image (ChSo): pixel / gray value / 8-32 bit / histogram / thresholding / filters
10:35-11:30 – brief intro to Image J (RoHa): find your way around in Image J / FIJI website
11:30-12:30 – lunch
12:30-13:25 – brief intro to Ilastik: image classification, segmentation and analysis (ChSo)
13:35-14:25 – Deconvolution (Huygens) & Airy scan (paper) processing (DoMi)
14:35-15:25 – Image-J / FIJI: useful plug-ins (RoHa)
15:35-16:30 – Intro to Imaris: modules and batch processing – new features in Imaris 9.3 (MoGo)
June 14, 2019
- hands on: Big Seminar room Ground floor / Office Bldg West
- lectures: Big Seminar room Ground floor / Office Bldg West
- hands on Q&A: BFB – i04.EG.035 – workstations 2, 4, 6, 7
09.30-11.00 – hands on: the basics of Image J macro programming (NaDa): website – make sure to install FIJI beforehand!!
11:00-12:00 – Image analysis with Content-Aware Image Restoration (C.A.R.E.) machine learning approaches (ChSo / RoHa): paper & website
12:00-13:00 – lunch
13:00-14:00 – Q&A @ workstation slot 1: WS 2, WS 4, WS6, WS7
14:00-15:00 – Q&A @ workstation slot 2: WS 2, WS 4, WS6, WS7
15:00-16:00 – Q&A @ workstation slot 3: WS 2, WS 4, WS6, WS7
PARTICIPANTS image analysis workshop 1 – 2019:
| name | lectures | Image-J macro | Q&A workstation | |
| registrations / availability | 29 / 30 |
20 /20 |
1 / 12 |
|
| 1 | Alexander Johnson | y | ||
| 2 | Alba JUANES GARCIA | y | – | |
| 3 | Aysan Cerag Yahya | y | ||
| 4 | Barbara Oliveira | y | y | |
| 5 | Bernadette Basilico | y | y | |
| 6 | Bettina Zens | y | y | – |
| 7 | Giselle CHEUNG | y | y | |
| 8 | Julia MICHALSKA | y | y | |
| 9 | Julian STOPP | y | ||
| 10 | Kasumi Kishi | y | y | |
| 11 | Katalin Szigeti | y | y | |
| 12 | Katarina Bartalska | – | ||
| 13 | Katarzyna Kumicz | y | – | |
| 14 | Marcia | y | y | |
| 15 | Lena Schwarz | y | ||
| 16 | Lisa Knaus | y | ||
| 17 | Michelle Gallei | y | – | |
| 18 | Mojtaba Tavakoli | y | y | |
| 19 | Nathalie Agudelo Dueñas | y | ||
| 20 | Nikola Canigova | y | y | |
| 21 | Patricia RODRIGUES | y | ||
| 22 | Peng Xia | y | y | PIV |
| 23 | Philipp Radler | y | ||
| 24 | Phillipp Velnecky | y | y | |
| 25 | Silvia Caballero | y | – | |
| 26 | Steffi Wachner | y | ||
| 27 | Suyash Naik | y | y | Imaris / Ilastik |
| 28 | Verena HÜBSCHMANN | y | y | |
| 29 | Zoe Dobler | y | y | |
| 30 | Medina Kordkut | y | – | |
| 31 | Robert Beattie | y | y |
|
| 32 | Jonna Hannele ALANKO | y |
|
|
| 33 |
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| 34 |
|
y = confirmed registration for the listed workshop topic