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| --- | ||
| layout: news-events | ||
| filename: events | ||
| title: April 2024 OME workshops | ||
| main-blurb: The OME Team gave two practical sessions on OMERO, OME-NGFF and IDR as a part of the Microscopy data analysis course at EMBL-EBI. | ||
| --- | ||
| <hr class="whitespace"> | ||
| <div class="row"> | ||
| <div class="column"> | ||
| <h2 class="event-day">Organisers: <a href="https://www.ebi.ac.uk/training/events/microscopy-data-analysis-machine-learning-and-bioimage-archive/" target="_blank">EMBL-EBI</a></h2> | ||
| </div> | ||
| </div> | ||
| <div class="row"> | ||
| <div class="column"> | ||
| <h2 class="event-day">Location: held remotely | ||
| </div> | ||
| </div> | ||
| <div class="row"> | ||
| <div class="column"> | ||
| <h2 class="event-day">Practical on Day 4: <a href="https://www.ebi.ac.uk/training/events/microscopy-data-analysis-machine-learning-and-bioimage-archive/#vf-tabs__section--tab2" target="_blank">Image data resource – practical</a> | ||
| </div> | ||
| </div> | ||
| <div class="row"> | ||
| <div class="column"> | ||
| <h2 class="event-day">Date: 25 April 2024</h2> | ||
| </div> | ||
| </div> | ||
| <div class="row"> | ||
| <div class="column"> | ||
| <h2 class="event-day">Duration: 3 hours</h2> | ||
| </div> | ||
| </div> | ||
| <div class="row"> | ||
| <div class="column"> | ||
| <h2 class="event-day">Practical on Day 5: <a href="https://www.ebi.ac.uk/training/events/microscopy-data-analysis-machine-learning-and-bioimage-archive/#vf-tabs__section--tab2" target="_blank">Distributed/Cloud computing - practical</a> | ||
| </div> | ||
| </div> | ||
| <div class="row"> | ||
| <div class="column"> | ||
| <h2 class="event-day">Date: 26 April 2024</h2> | ||
| </div> | ||
| </div> | ||
| <div class="row"> | ||
| <div class="column"> | ||
| <h2 class="event-day">Duration: 3 hours</h2> | ||
| </div> | ||
| </div> | ||
| <hr class="whitespace"> | ||
| <div class="row"> | ||
| <div class="column"> | ||
| <p class="event-day-description">The usage of <a href="https://idr.openmicroscopy.org" target="_blank">Image Data Resource (IDR)</a> was explored and it was demonstrated how to access the IDR data using the Python API, to fetch image data and metadata from IDR study associated with a publication. A workflow involving programmatical harvesting of data from multiple Data resources (<a href="https://www.humanmine.org/humanmine" target="_blank">HumanMine</a> and <a href="https://idr.openmicroscopy.org" target="_blank">IDR</a>) was shown. Further, re-analysis of data using an alternative segmentation tool to the one used by the publication authors was performed. The analytical packages used included <a href="https://www.cellpose.org/" target="_blank">Cellpose</a>, <a href="https://github.com/stardist/stardist" target="_blank">StarDist</a> and <a href="https://cellprofiler.org/" target="_blank">CellProfiler</a>. In the second workshop on the following day, the Distributed/Cloud computing workshop introduced an emerging cloud-optimized imaging format <a href="https://ngff.openmicroscopy.org" target="_blank">OME-NGFF</a> currently used by the <a href="https://www.ebi.ac.uk/bioimage-archive/" target="_blank">BioImage Archive</a> and the <a href="https://idr.openmicroscopy.org" target="_blank">IDR</a>. It was shown how it can be used to access cloud-hosted imaging data and how it facilitates analysis in parallel, how to convert other formats into OME-NGFF and how to upload and download OME-NGFF images to and from S3 storage. The image analysis examples included workflows involving <a href="https://www.cellpose.org/" target="_blank">Cellpose</a> and <a href="https://github.com/stardist/stardist" target="_blank">StarDist</a>. | ||
| </p> | ||
| </div> | ||
| </div> | ||
| <hr class="whitespace"> | ||
| <div class="row"> | ||
| <div class="column"> | ||
| <h2 class="event-day">Resources available:</h2> | ||
| <p class="event-day-description">The <a href="https://github.com/ome/EMBL-EBI-imaging-course-04-2024" target="_blank">repository with jupyter notebooks and scripts</a> and five selected workflows published on WorkflowHub. <br> | ||
| <ol> | ||
| <li><a href="https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.489.1" target="_blank">Load Image with labels from IDR, re-analyze using Cellpose | ||
| </a><br></li> | ||
| <li><a href="https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.493.1" target="_blank">Load Image with labels from IDR, re-analyze using StarDist | ||
| </a><br></li> | ||
| <li><a href="https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.495.1" target="_blank">Load ome.zarr Image with labels from public S3 repositories, analyze in parallel using Cellpose and compare results | ||
| </a><br></li> | ||
| <li><a href=" https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.496.1" target="_blank">Load ome.zarr Image with labels from a public S3 repository, analyze using StarDist and compare results | ||
| </a><br></li> | ||
| <li><a href="https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.494.1" target="_blank">Use Public Resources to answer a biological question | ||
| </a><br></li> | ||
| </ol></p> | ||
| </div> | ||
| </div> |