We will learn how to use conv-paint, a fast and interactive pixel classification tool for multi dimensional images. A graphical user interface is integrated into the image viewer napari, but we will also learn how to script the software from the python ecosystem. As a napari-plugin, conv-paint can easily be integrated with other plugins into complex image processing pipelines, even by users...
CAREamics is a modern re-implementation of widely used algorithms (CARE, N2N, N2V) and of more recent methods (DivNoising, HDN, muSplit, etc.), with a strong emphasis on usability for non-specialists. In this workshop, we will walk users through standard pipelines, how to approach a denoising task, which methods to choose and the various ways to use CAREamics, including via its napari UI.
This workshop will delve into the innovative features of NanoPyx, a Python framework designed to streamline microscopy image analysis. Participants will have hands-on experience on the image analysis methods implemented in NanoPyx, such as image registration, super-resolution and quality metrics, using the multiple user interfaces of NanoPyx: napari plugin, Jupyter notebooks and python...
We believe that FeatureForest addresses some of the shortcomings of both deep learning approaches and classical classifiers. While not a novelty, coupling deep-learning features and random forest allows complex biological objects to be segmented easily, without the need for extensive manual data labeling or expert deep-learning knowledge. We want to advertise the tool as it can be helpful to...
In this workshop, we would like to introduce the functionalities of MemBrain v2 and demonstrate its handling using some showcase examples.
We will introduce MemBrain v2's three main components: MemBrain-seg is our out-of-the-box U-Net that gives good segmentations on a wide variety of tomograms. MemBrain-pick closely interacts with an annotation software to enable interactive training and...
QuPath is a popular open-source platform for visualizing, annotating and analyzing complex images - including whole slide and highly multiplexed datasets. QuPath is written in Java and scriptable with Groovy, which makes it portable, powerful, and... sometimes a pain if you aren't a programmer. It can also be annoying if you are a programmer, but you find Groovy's syntax weird { and...
Based on the NEUBIAS (bio image analysts) and COMULIS (Correlated Multimodal Imaging in Life science) community effort, we have build a data base of image analysis software, aiming to be feed and used by the community. In this workshop, we will show how to search efficiently for an existing tool in bio image analysis, how to add a new tool or ressource and how to curate an existing entry,...
