Skip to content

Latest commit

 

History

History
50 lines (27 loc) · 2.5 KB

Use_Cases.md

File metadata and controls

50 lines (27 loc) · 2.5 KB

Use Cases & Test Data

Please describe, link to and/or list all Use Cases and examples of application here regardless if these are complete or in progress.

Please list/link also to Use Cases described in the topic's directories to obtain a comprehensive list here.

Electron Microscopy (Mitochondria in HeLa cells)

Work with a focus on metadata transfer by @pzentis.

Images with ISA/ARC like metadata as key-value-pairs in a project/dataset structure.

One KVP-list per excel sheet:

In Omero (only available in UoC campus network):
https://omero-3-web.cecad.uni-koeln.de/webclient/?show=project-1305

The omero-links only work in the Cologne campus network (including eduroam), see here for Omero access details: Omero accounts

You can import this project in your own Omero server by omero-cli-transfer using this tarball: file, 700MB

One KVP-list per ISA-section and and entry:

In Omero (only available in UoC campus network):
https://omero-3-web.cecad.uni-koeln.de/webclient/?show=project-1304

The omero-links only work in the Cologne campus network (including eduroam), see here for Omero access details: Omero accounts

You can import this project in your own Omero server by omero-cli-transfer using this tarball: file, 700MB

Corresponding pseudo-ARC folder structure, csv-tables to import KVPs...

https://github.com/cecad-imaging/omero-arc-testdata

CLSM stacks

Here you can find @andreaschrader's ARC in the making: https://git.nfdi4plants.org/natural-variation-and-evolution/microscopy_collection/map-by-seq_clsm-stacks

Please note, Swate annotation is not completed and is WIP.

Spatial Transcriptomics

Here you can find a nice ARC created by @MicheleBortol: https://git.nfdi4plants.org/michele.bortolomeazzi/mben_resolve

REMBI

The example REMBI file derived from an ARC in which a template based on experiences of the CAi @HHU Duesseldorf, Germany was filled by @Tom-TBT, @VAFuchs and @andreaschrader in the REMBI-Mapping group is located here. This example was based on this ARC.