The project allowed us to manage and build structured code scripts on the Jupyter Notebook, a simple web application which is user-friendly, flexible to use in the research community. The script is developed to address the specific needs of research between different platforms of dataset. These stakeholders have developed their own platforms for the annotation and standardisation of both data and metadata produced within their respective field. -The INFRAFRONTIER - European Mutant Mouse Archive ...

CroMaSt: A workflow for assessing protein domain classification by cross-mapping of structural instances between domain databases and structural alignment

CroMaSt (Cross Mapper of domain Structural instances) is an automated iterative workflow to clarify the assignment of protein domains to a given domain type of interest, based on their 3D structure and by cross-mapping of domain structural instances between domain databases. CroMaSt (for Cross-Mapper of domain Structural instances) ...

This workflow has been created as part of Demonstrator 6 of the project EOSC-Life (within WP3) and is focused on reusing publicly available RNAi screens to gain insights into the nucleolus biology. The workflow downloads images from the Image Data Resource (IDR), performs object segmentation (of nuclei and nucleoli) and feature extraction of the images and objects identified.

Tutorial: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/tutorial-CP/tutorial.html

Gene similariy anaylsis across physiological systems in IMPC phenotype data

A Jupyter Notebook tool for analysing user specified genes across the different physiological systems in IMPC data.

Input

The tool takes as input a list of gene ids (MGI ids or Gene Symbol ids). The elemnts in the list could be separated by a comma, semicolumn, tab or newline.

Operation

The program will create an heatmap representing the number of phenotypes and the mp term list for each gene contained in ...

Introduction

This repository contains all the custom scripts used in the evaluation and comparison of Katdetectr as described in the corresponding Technical Note (under submission).

Usage

All required files were deposited on Zenodo. These can directly be downloaded using zen4R and be used as input.

# Increase the timeout (due to some large files). 
options(timeout=5000)
...

The image is referenced in the paper "NesSys: a novel method for accurate nuclear segmentation in 3D" published August 2019 in PLOS Biology: https://doi.org/10.1371/journal.pbio.3000388 and can be viewed online in the Image Data Resource.

This original image was converted into the Zarr format. The analysis results produced by the authors of the paper were converted into labels and linked to the Zarr file which was placed into a public ...

Learning objectives

• Read data to analyse from an object store.
• Analyse data in parallel using Dask.
• Show how to use public resources to train neural network.
• Load labels associated to the original data
• Compare results with ground truth.

The authors of the PLOS Biology paper, "Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures" published in August 2019: https://doi.org/10.1371/journal.pbio.3000388, considered several image ...

IDR is based on OMERO and thus all what we show in this notebook can be easily adjusted for use against another OMERO server, e.g. your institutional OMERO server instance.

The main objective of this notebook is to demonstrate how public resources such as the IDR can be used to train your neural network or validate software tools.

The authors of the PLOS Biology paper, "Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures" published in August ...