OME
OverviewSoftware and data format standards for management of microscopy image data. Joint project between international private and public research
Space: Independent Teams
SEEK ID: https://workflowhub.eu/projects/69
Public web page: https://www.openmicroscopy.org/
Organisms: Homo sapiens, Sars-cov-2
WorkflowHub PALs: No PALs for this Team
Team created: 4th Nov 2021
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Teams: OME, Euro-BioImaging
Organizations: University of Dundee, Euro-BioImaging
https://orcid.org/0000-0001-8783-1429
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Web page: Not specified
Creator: Jean-Marie Burel
Submitter: Jean-Marie Burel
External Link
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 ...
Type: Unrecognized workflow type
Creators: Jean-Marie Burel, Petr Walczysko
Submitter: Jean-Marie Burel
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 ...
Type: Unrecognized workflow type
Creators: Jean-Marie Burel, Petr Walczysko
Submitter: Jean-Marie Burel
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 ...
Learning Objectives
- How to access genomic resource via its Python API
- How to access image resource via its Python API
- Relate image data to genomic data
Diabetes related genes expressed in pancreas
This notebook looks at the question Which diabetes related genes are expressed in the pancreas? Tissue and disease can be modified.
Steps:
- Query humanmine.org, an integrated database of Homo sapiens genomic data using the intermine API to find the ...
The notebook shows how to load an IDR image with labels.
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.
In this notebook, the image is loaded together with the labels and analyzed using StarDist. The StarDist analysis produces a segmentation, which is then viewed side-by-side with the original segmentations ...
Type: Unrecognized workflow type
Creators: Jean-Marie Burel, Petr Walczysko
Submitter: Jean-Marie Burel
Summary
This notebook demonstrates how to recreate lineages published in the paper Live imaging of remyelination in the adult mouse corpus callosum and available at idr0113-bottes-opcclones.
The lineage is created from the metadata associated to the specified image.
To load the data from the Image Data Resource, we use:
- the Python API ...
Summary
This notebook shows how to integrate genomic and image data resources. This notebook looks at the question Which diabetes related genes are expressed in the pancreas?
Steps:
- Query humanmine.org, an integrated database of Homo sapiens genomic data using the intermine API to find the genes.
- Using the list of found genes, search in the Image Data Resource (IDR) for images linked to the genes, tissue and disease.
We use the intermine API and the IDR API
The notebook can be launched ...
DownloadSummary
This notebook demonstrates how to retrieve metadata associated to the paper A SARS-CoV-2 cytopathicity dataset generated by high-content screening of a large drug repurposing collection and available in IDR at idr0094-ellinger-sarscov2. Over 300 compounds were used in this investigation. This notebook allows the user to calculate the half maximal inhibitory concentration (IC50) for ...
Collection of workflows exploring data in the Image Data Resource (IDR).
