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I2K Conference
Приєднався 16 лют 2022
For more details about the I2K Conference visit i2kconference.org or contacts us at i2kconference@gmail.com.
Leveraging Cloud-Based Virtual Desktops for Bioimage Analysis with BAND and DeepImageJ
Leveraging Cloud-Based Virtual Desktops for Bioimage Analysis with BAND and DeepImageJ | Yi Sun, Caterina Fuster-Barceló | October 17th, Halfway to I2K 2023
Authors: - Yi Sun, European Molecular Biology Laboratory (EMBL);
- Caterina Fuster-Barceló ,Universidad Carlos III Madrid(UC3M)
Description: The first part of the session will provide an overview of the platform. Following this, a demonstration will showcase the application DeepImageJ for analyzing a sample image within the platform
Keywords: Cloud desktop, image analysis, deep learning,DeepImageJ
Authors: - Yi Sun, European Molecular Biology Laboratory (EMBL);
- Caterina Fuster-Barceló ,Universidad Carlos III Madrid(UC3M)
Description: The first part of the session will provide an overview of the platform. Following this, a demonstration will showcase the application DeepImageJ for analyzing a sample image within the platform
Keywords: Cloud desktop, image analysis, deep learning,DeepImageJ
Переглядів: 238
Відео
Introduction to BiofilmQ: File import, threshold-based cube segmentation and basic parameter calcs
Переглядів 13111 місяців тому
Introduction to BiofilmQ: File import, threshold-based cube segmentation and basic parameter calculations | Eva Jiménez-Siebert | October 17th, Halfway to I2K 2023 Authors: Eva Jiménez-Siebert, Biozentrum, University of Basel, Basel, Switzerland; Hannah Jeckel, California Institute of Technology, Pasadena, California, USA; Niklas Netter, Biozentrum, University of Basel, Basel, Switzerland; Knut...
Reproducible figures with Inkscape, R, Python and ImageJ
Переглядів 43611 місяців тому
Reproducible figures with Inkscape, R, Python and ImageJ | Jerome Mutterer | October 17th, Halfway to I2K 2023 Authors: Jerome Mutterer, CNRS Description: I would introduce participants to using Inkscape to create figures, slides or posters that display both the usual design elements but also some level of reproducible content where this is possible. This means figure panels with images, graphs...
Scaling AI-powered Bioimage Analysis with the BioEngine
Переглядів 10911 місяців тому
Scaling AI-powered Bioimage Analysis with the BioEngine | Wei OUYANG | October 17th, Halfway to I2K 2023 Authors: Wei Ouyang, KTH Royal Institute of Technology Jeremy Metz, KTH Royal Institute of Technology Craig Russell, EMBL-EBI Description: The workshop aims to provide a tour on using BioEngine, a container based cloud service framework for running AI models, for performing web- and cloud-ba...
Scientific Figure Making with Fiji and Inkscape
Переглядів 1,8 тис.11 місяців тому
Scientific Figure Making with Fiji and Inkscape | Jan Brocher | October 17th, Halfway to I2K 2023 Authors: Jan Brocher, BioVoxxel Description: This workshop will communicate methods for best practice in publication figure creation from scientific images. It combines the easy to use BioVoxxel Figure Tools plugin for Fiji with Inkscape for final figure composition and explains crucial considerati...
OMERO.figure for reproducible figures within the data management platform OMERO
Переглядів 21111 місяців тому
OMERO.figure for reproducible figures within the data management platform OMERO | Tom Boissonnet | October 17th, Halfway to I2K 2023 Authors: Tom Boissonnet, Heinrich Heine Universität, Düsseldorf Description: In this workshop, we will learn how to make figures with OMERO.figure, a plugin for the web-browser client of the research data management platform OMERO. We will show how that tool benef...
Introduction to FAIR Container-based Workflows in Web Image Processing Pipeline (WIPP)
Переглядів 13011 місяців тому
Introduction to FAIR Container-based Workflows in Web Image Processing Pipeline (WIPP) | Mylene Simon & Peter Bajcsy | October 17th, Halfway to I2K 2023 Authors: Mylene Simon and Peter Bajcsy National Institute of Standards and Technology (NIST) Description: This tutorial will overview a Web Image Processing Pipeline (WIPP) platform for running Findable Accessible Interoperable and Reusable (FA...
Introduction to Nyxus: A Feature-Rich, Highly Optimized Feature Extraction Library
Переглядів 7911 місяців тому
Introduction to Nyxus: A Feature-Rich, Highly Optimized Feature Extraction Library | Sameeul Samee | October 17th, Halfway to I2K 2023 Authors: Sameeul B Samee, Axle Research and Technologies Description: This workshop will provide an introduction to Nyxus. We will look at the installation process, various API to feed images for feature extraction, how to use different output formats for storag...
napari-imagej: using ImageJ inside Python's napari data viewer
Переглядів 61811 місяців тому
napari-imagej: using ImageJ inside Python's napari data viewer | Gabriel Selzer | October 17th, Halfway to I2K 2023 Authors: Gabriel J. Selzer, University of Wisconsin-Madison; Curtis T. Rueden, University of Wisconsin-Madison; Marck C. Hiner, University of Wisconsin-Madison; Edward L. Evans III, University of Wisconsin-Madison, Morgridge Institute for Research; Kyle I. S. Harrington, Chan Zuck...
Introduction to Cell Profiler: A beginner’s guide to segmentation
Переглядів 1,7 тис.11 місяців тому
Introduction to Cell Profiler: A beginner’s guide to segmentation | Shatavisha Dasgupta | October 17th, Halfway to I2K 2023 Authors: Shatavisha Dasgupta, Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA Description: Quantitative analysis of optical microscopy images is the cornerstone of modern day biological research. A working knowledge of image analysis and familiarit...
napari-signal-selector: a plugin to interactively annotate signals from object features in napari
Переглядів 14811 місяців тому
napari-signal-selector: a plugin to interactively annotate signals from object features in napari | Marcelo Leomil Zoccoler | October 18th, Halfway to I2K 2023 Authors: Marcelo Leomil Zoccoler, Bio-image Analysis Technology Development DFG Cluster of Excellence “Physics of Life” TU Dresden Description: This workshop will showcase napari-signal-selector, a plugin built with napari-matplotlib bac...
Machine Learning and Deep Learning for Dummies
Переглядів 60411 місяців тому
Machine Learning and Deep Learning for Dummies | Aryeh Weiss | October 18th, Halfway to I2K 2023 Authors: Aryeh Weiss Description: Machine learning (ML) and deep learning (DL) tools are now available that allow non-experts to apply these technologies. This workshop describes one such dummy's experience applying ML and DL to segmentation of plant images and stem cross-sections. The tools that ar...
Generative Artificial Intelligence for Bio-image Analysis
Переглядів 38311 місяців тому
Generative Artificial Intelligence for Bio-image Analysis | Robert Haase | October 17th, Halfway to I2K 2023 Authors: Robert Haase, ScaDS.AI / Uni Leipzig, PoL / TU Dresden Description: Generative Artificial Intelligence - and in particular large languge models - are changing the way we use computers. In this workshop we will go through the underlying principles and give examples how large lang...
Analysis of Spatial Transcriptomics data
Переглядів 83711 місяців тому
Analysis of Spatial Transcriptomics data | Levin Moser | October 18th, Halfway to I2K 2023 Authors: Levin Moser, Broad Institute Description: This workshop gives an introduction on how to analyze Spatial Transcriptomics data. We will go step-by-step through a basic analysis pipeline using Python and a public MERFISH dataset. These steps include data normalization, quality control, clustering, a...
What's new in QuPath v0.5?
Переглядів 2,3 тис.11 місяців тому
What's new in QuPath v0.5? | Peter Bankhead | October 18th, Halfway to I2K 2023 Authors: Peter Bankhead, University of Edinburgh Description: In recent years, QuPath has become one of the most widely-used open-source software platforms for bioimage analysis, as well as a frequent topic of discussion on image.sc. Although originally designed to work with whole slide images, QuPath's distinctive ...
Exploring the Intersection of Deconvolution, GPU Computing, and Deep Learning
Переглядів 23111 місяців тому
Exploring the Intersection of Deconvolution, GPU Computing, and Deep Learning
Introduction to CellProfiler Analyst
Переглядів 96711 місяців тому
Introduction to CellProfiler Analyst
Collaborative annotation of large 3D images with WEBKNOSSOS
Переглядів 14811 місяців тому
Collaborative annotation of large 3D images with WEBKNOSSOS
Advanced BiofilmQ analysis pipelines: Curating, importing and analyzing single-cell segmentations
Переглядів 14211 місяців тому
Advanced BiofilmQ analysis pipelines: Curating, importing and analyzing single-cell segmentations
Introducing Piximi - Image Classification and Segmentation in the Browser
Переглядів 17711 місяців тому
Introducing Piximi - Image Classification and Segmentation in the Browser
Unlock the Potential of Your Microscopy Images with Morpheus Software!
Переглядів 14611 місяців тому
Unlock the Potential of Your Microscopy Images with Morpheus Software!
Fundamentals of image analysis in Python with scikit-image, napari, and friends
Переглядів 45411 місяців тому
Fundamentals of image analysis in Python with scikit-image, napari, and friends
Using Fiji/MoBIE for visual QC of CellProfiler and ilastik output
Переглядів 16411 місяців тому
Using Fiji/MoBIE for visual QC of CellProfiler and ilastik output
3D Segmentation using CellProfiler
Переглядів 1,5 тис.11 місяців тому
3D Segmentation using CellProfiler
Advanced BiofilmQ analysis and visualization
Переглядів 11911 місяців тому
Advanced BiofilmQ analysis and visualization
Introduction to ultrack, Cell Tracking in Python Under Segmentation Uncertainty
Переглядів 65511 місяців тому
Introduction to ultrack, Cell Tracking in Python Under Segmentation Uncertainty
ZEISS Open-Source software tools and Python packages for CZI images and deep-learning models
Переглядів 49011 місяців тому
ZEISS Open-Source software tools and Python packages for CZI images and deep-learning models
Bioimage analysis with Python and napari
Переглядів 30111 місяців тому
Bioimage analysis with Python and napari
PyImageJ: Integrating ImageJ/Fiji with the Python ecosystem
Переглядів 1,6 тис.11 місяців тому
PyImageJ: Integrating ImageJ/Fiji with the Python ecosystem
Considine Mountains
Is this able to do the segmentation of the complex cell types
Plz provide me code
Thanks for the videos!! I would like to know what are the system requirements of a pc laptop to run the software smoothly? I would appreciate a reference in terms of memory, processor, cpu and graphic card, I did not find on the net current data for 2024 version 5.1 Thanks 
first like and exactly on topic. Me likey.
This is a life saver. Thank you Jan!
Edward, this is great info! One question I have is your recommendation for the easiest way to capture image data going back and forth between python and imagej. For example, in tutorial 6 working with images, I see how I can open the test_timeseries.tif and open it in my local FIJI and operating in interactive mode. If I do a median filter, max intensity projection and then flatten that image, how can I transfer that new image from that new window into python to display and process it further? I don't see how I can make that new window the active image or what that new window variable is or do I need to save that new window first? Thanks!
One follow up question related to this is what do you recommend for running Imagej in a debug mode? Seems that being able to set breakpoints and see variable names for both python as well as java would be immensely helpful to being able to bounce back and forth. Since I have used Imagej quite a bit for many years, that is my go to program. But there are many times that image processing in python would be extremely helpful, though I would transfer everything back into Imagej before saving my images.
F❤
The NEW update site is called BioVoxxel Figure Tools in the Fiji update site list
Good afternoon! Thanks for your videos! 🙂 Could you please answer, is the macbook air m1 enouth to work well with qupath? Or I have to buy more powerful laptop? I will be grateful for the answer!
Excelent talk and tutorials!
Link to wiki: imagej.net/plugins/labkit/
Link to repository: github.com/schmiedc/SynActJ
Link to github pages: schmiedc.github.io/SynActJ/