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title Catalog of IDR images formatted as OME-NGFF
layout default
<script type="application/ld+json"> { "@context": "http://schema.org", "@type": "DataCatalog", "inLanguage": "en-US", "name": "IDR OME-NGFF Samples", "publisher": { "@type": "Organization", "name": "GitHub" }, "copyrightYear": "2022", "discussionUrl": "https://github.com/IDR/ome-ngff-samples/issues", "accessMode": "visual", "measurementTechnique": "microscopy" } </script> <style> .page-content .wrapper { box-sizing: border-box; width: 100%; max-width: 100%; } .dataTables_scrollHeadInner { margin: 0 auto; } .icon { width: 24px; height: 24px; } .icon.vizarr { width: 27px; } .no_border { border: none; background: none; padding: 0; } .shake { animation: 0.1s linear 0s infinite alternate seesaw; } .bff { display: inline-block; padding: 0.25em 0.5em; border: 1px solid #ccc; border-radius: 10px; background-color: #f9f9f9; text-decoration: none; font-size: 0.9em; } @-webkit-keyframes seesaw { from { transform: rotate(-0.05turn) } to { transform: rotate(0.05turn); } } @keyframes seesaw { from { transform: rotate(-0.05turn) } to { transform: rotate(0.05turn); } } </style>

Download or Access Data

Click the copy button in the table below for download options including URLs and code samples. You can also open this table in BioFile Finder.

{% assign s3key = "File Path" %} {% assign studykey = "Study" %} {% for rec in site.data.table %} {% capture image_name %}{{ rec[s3key] | split: "/" | last }}{% endcapture %} {% capture image_id %}{{ image_name | split: "." | first}}{% endcapture %} {% endfor %}
OME-NGFF version Thumbnail EMBL-EBI S3 key SizeX SizeY SizeZ SizeC SizeT Axes Wells Fields Keywords License Study DOI Date added
{{ rec["OME-NGFF version"] }} IDR thumbnail for Image:{{ rec[ {{ image_name }}
{% if rec['Wells'] or rec['Keywords'] != "bioformats2raw.layout" %} {% endif %} {% unless rec['Wells'] %} {% unless rec["OME-NGFF version"] == "0.1" or rec["OME-NGFF version"] == "0.2" or rec["OME-NGFF version"] == "0.3" %} {% endunless %} {% endunless %} 		{{ rec["SizeX"] }} {{ rec["SizeY"] }} {{ rec["SizeZ"] }} {{ rec["SizeC"] }} {{ rec["SizeT"] }} {{ rec["Axes"] }} {{ rec["Wells"] }} {{ rec["Fields"] }} {{ rec["Keywords"] }} {{ rec["License"] }} {{ rec["Study"] }}
{% if rec["Wells"] %} {% else %} {% endif %} 		{{ rec["DOI"] }} {{ rec["Date added"] }}
<script> $(document).ready( function () { $('#table').DataTable( { "scrollX": true, "pageLength": 100, "order": [[ 15, 'desc' ]], "fixedHeader": true }); } ); function generatePythonCode(httpsUrl) { const s3Url = httpsUrl.replace('https://livingobjects.ebi.ac.uk/', 's3://'); const endpoint = 'https://livingobjects.ebi.ac.uk'; const code = `import zarr zarr_group = zarr.open( "${s3Url}", storage_options={ "anon": True, "client_kwargs": { "endpoint_url": "${endpoint}" } } )`; const html = `import zarr zarr_group = zarr.open( "${s3Url}", storage_options={ "anon": True, "client_kwargs": { "endpoint_url": "${endpoint}" } } )`; return { code, html }; } function showS3Options(httpsUrl, imageName) { const s3Url = httpsUrl.replace('https://livingobjects.ebi.ac.uk/', 's3://'); const endpoint = 'https://livingobjects.ebi.ac.uk'; const awsCommand = `aws s3 sync --endpoint-url ${endpoint} --no-sign-request ${s3Url} ${imageName}`; const omeZarrCommand = `uvx --with ome-zarr ome_zarr download ${httpsUrl} --output ${imageName}`; const python = generatePythonCode(httpsUrl); const modal = document.getElementById('s3OptionsModal'); document.getElementById('s3OptionsTitle').textContent = `Download Options: ${imageName}`; document.getElementById('awsCliCommand').textContent = awsCommand; document.getElementById('omeZarrCommand').textContent = omeZarrCommand; document.getElementById('s3Endpoint').textContent = endpoint; document.getElementById('s3UrlText').textContent = s3Url; document.getElementById('httpsUrlText').textContent = httpsUrl; document.getElementById('pythonCodeInOptions').innerHTML = python.html; document.getElementById('awsCliCommand').dataset.copyText = awsCommand; document.getElementById('omeZarrCommand').dataset.copyText = omeZarrCommand; document.getElementById('s3Endpoint').dataset.copyText = endpoint; document.getElementById('s3UrlText').dataset.copyText = s3Url; document.getElementById('httpsUrlText').dataset.copyText = httpsUrl; document.getElementById('pythonCodeInOptions').dataset.copyText = python.code; modal.style.display = 'block'; modal.onclick = closeS3Options; } function closeS3Options(event) { // event is undifined if click comes from x button if (event == undefined || event?.target.id == "s3OptionsModal") { document.getElementById('s3OptionsModal').style.display = 'none'; } } function copyFromDataset(element) { copyTextToClipboard(element.dataset.copyText); } function copyTextToClipboard(text) { var textArea = document.createElement("textarea"); // Place in the top-left corner of screen regardless of scroll position. textArea.style.position = 'fixed'; textArea.value = text; document.body.appendChild(textArea); textArea.focus(); textArea.select(); var successful; try { successful = document.execCommand('copy'); } catch (err) { console.log('Oops, unable to copy'); } document.body.removeChild(textArea); if (successful) { // Show "Copied!" feedback to the left of button let target = event.target; let feedback = document.createElement('span'); feedback.textContent = 'Copied! '; feedback.style.color = '#28a745'; feedback.style.fontSize = '12px'; feedback.style.marginRight = '5px'; target.parentNode.insertBefore(feedback, target); setTimeout(() => { feedback.remove(); }, 1500) } else { console.log("Copying failed") } } </script>

Download Options

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    <div style="margin-bottom: 20px; padding: 15px; border: 3px solid #e0e0e0; border-radius: 5px;">
        <div style="display: flex; justify-content: space-between; align-items: center; margin-bottom: 5px; gap: 10px;">
            <h4 style="margin: 0;">HTTPS URL:</h4>
            <div style="display: flex; align-items: center;">
                <button onclick="copyFromDataset(document.getElementById('httpsUrlText'))" style="padding: 6px 12px; cursor: pointer; background: #0066cc; color: white; border: none; border-radius: 3px; font-size: 12px;">
                    Copy
                </button>
            </div>
        </div>
        <code id="httpsUrlText" style="display: block; padding: 10px; background: #f5f5f5; border-radius: 3px; overflow-x: auto; white-space: nowrap;"></code>
    </div>

    <div style="margin-bottom: 20px; padding: 15px; border: 3px solid #e0e0e0; border-radius: 5px;">
        <div style="display: flex; justify-content: space-between; align-items: center; margin-bottom: 5px; gap: 10px;">
            <h4 style="margin: 0;"><a href="https://ome-zarr.readthedocs.io/en/stable/index.html" target="_blank" style="color: #0066cc; text-decoration: underline;">ome-zarr</a> CLI Command:</h4>
            <div style="display: flex; align-items: center;">
                <button onclick="copyFromDataset(document.getElementById('omeZarrCommand'))" style="padding: 6px 12px; cursor: pointer; background: #0066cc; color: white; border: none; border-radius: 3px; font-size: 12px;">
                    Copy
                </button>
            </div>
        </div>
        <code id="omeZarrCommand" style="display: block; padding: 10px; background: #f5f5f5; border-radius: 3px; overflow-x: auto; white-space: nowrap;"></code>
    </div>

    <div style="margin-bottom: 20px; padding: 15px; border: 3px solid #e0e0e0; border-radius: 5px;">
        <div style="display: flex; justify-content: space-between; align-items: center; margin-bottom: 5px; gap: 10px;">
            <h4 style="margin: 0;">AWS CLI Command:</h4>
            <div style="display: flex; align-items: center;">
                <button onclick="copyFromDataset(document.getElementById('awsCliCommand'))" style="padding: 6px 12px; cursor: pointer; background: #0066cc; color: white; border: none; border-radius: 3px; font-size: 12px;">
                    Copy
                </button>
            </div>
        </div>
        <code id="awsCliCommand" style="display: block; padding: 10px; background: #f5f5f5; border-radius: 3px; overflow-x: auto; white-space: nowrap;"></code>
    </div>

    <div style="margin-bottom: 20px; padding: 15px; border: 3px solid #e0e0e0; border-radius: 5px;">
        <div style="margin-bottom: 20px;">
            <div style="display: flex; justify-content: space-between; align-items: center; margin-bottom: 5px; gap: 10px;">
                <h4 style="margin: 0;">S3 Endpoint URL:</h4>
                <div style="display: flex; align-items: center;">
                    <button onclick="copyFromDataset(document.getElementById('s3Endpoint'))" style="padding: 6px 12px; cursor: pointer; background: #0066cc; color: white; border: none; border-radius: 3px; font-size: 12px;">
                        Copy
                    </button>
                </div>
            </div>
            <code id="s3Endpoint" style="display: block; padding: 10px; background: #f5f5f5; border-radius: 3px; overflow-x: auto;"></code>
        </div>

        <div style="margin-bottom: 0;">
            <div style="display: flex; justify-content: space-between; align-items: center; margin-bottom: 5px; gap: 10px;">
                <h4 style="margin: 0;">S3 URL:</h4>
                <div style="display: flex; align-items: center;">
                    <button onclick="copyFromDataset(document.getElementById('s3UrlText'))" style="padding: 6px 12px; cursor: pointer; background: #0066cc; color: white; border: none; border-radius: 3px; font-size: 12px;">
                        Copy
                    </button>
                </div>
            </div>
            <code id="s3UrlText" style="display: block; padding: 10px; background: #f5f5f5; border-radius: 3px; overflow-x: auto;"></code>
        </div>
    </div>

    <div style="margin-bottom: 0; padding: 15px; border: 3px solid #e0e0e0; border-radius: 5px;">
        <div style="display: flex; justify-content: space-between; align-items: center; margin-bottom: 5px; gap: 10px;">
            <h4 style="margin: 0;"><a href="https://zarr.readthedocs.io/en/stable/" target="_blank" style="color: #0066cc; text-decoration: underline;">Zarr-Python</a>:</h4>
            <div style="display: flex; align-items: center;">
                <button onclick="copyFromDataset(document.getElementById('pythonCodeInOptions'))" style="padding: 6px 12px; cursor: pointer; background: #0066cc; color: white; border: none; border-radius: 3px; font-size: 12px;">
                    Copy
                </button>
            </div>
        </div>
        <pre id="pythonCodeInOptions" style="margin: 0; padding: 15px; background: #f5f5f5; border-radius: 3px; overflow-x: auto;"></pre>
    </div>
</div>