https://wiki.bwhpc.de/wiki/index.php?action=history&feed=atom&title=Helix%2FbwVisu%2FQuPath 2026-04-06T22:19:35Z Revision history for this page on the wiki MediaWiki 1.39.17 https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/QuPath&diff=15267&oldid=prev 2025-09-02T14:44:58Z

<p>Added troubleshooting section</p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:44, 2 September 2025</td> </tr><tr> <td colspan="2" class="diff-lineno">Line 27:</td> <td colspan="2" class="diff-lineno">Line 27:</td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* Go to Edit &gt; Preferences &gt; Cellpose/Omnipose</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* Go to Edit &gt; Preferences &gt; Cellpose/Omnipose</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* Add the path to the Python executable: "/opt/cellpose/bin/python3.9"</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* Add the path to the Python executable: "/opt/cellpose/bin/python3.9"</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><br /></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>== Troubleshooting ==</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><br /></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*'''Main window doesn't stay full size when other windows open'''</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>:-&gt; Enlarge the main QuPath window with the mouse, instead of clicking on the "maximize" button.</div></td> </tr> </table>

H Schumacher https://wiki.bwhpc.de/wiki/index.php?title=Helix/bwVisu/QuPath&diff=15266&oldid=prev 2025-09-02T14:26:09Z

<p>Instructions for adding the Cellpose extension</p> <p><b>New page</b></p><div>{|style=&quot;background:#ffdeee; width:100%;&quot;<br /> |style=&quot;padding:5px; background:#f2cece; text-align:left&quot;|<br /> [[Image:Attention.svg|center|25px]]<br /> |style=&quot;padding:5px; background:#f2cece; text-align:left&quot;|<br /> GPU support and CellPose are work in progress. <br /> |}<br /> [https://qupath.readthedocs.io/en/stable/index.html QuPath] offers a powerful set of tools for a wide range of image formats, including many whole slide formats.<br /> <br /> __FORCETOC__<br /> <br /> == Add [https://qupath.readthedocs.io/en/latest/docs/intro/extensions.html Extensions] ==<br /> <br /> <br /> <br /> === CellPose ===<br /> <br /> The official installation and usage instructions for the extension can be found at https://github.com/BIOP/qupath-extension-cellpose.<br /> <br /> To summarize: <br /> # Install Cellpose<br /> #* Cellpose and the extra dependency scikit-image are already installed. This step can be skipped. <br /> # Add the extension<br /> ## Install and setup the [https://github.com/BIOP/qupath-biop-catalog?tab=readme-ov-file#installation qupath-biop-catalog]<br /> ## Add the Cellpose extension (Extensions -&gt; Manage Extensions)<br /> ## Restart QuPath / the bwVisu Job<br /> # First time setup<br /> #* Go to Edit &gt; Preferences &gt; Cellpose/Omnipose<br /> #* Add the path to the Python executable: &quot;/opt/cellpose/bin/python3.9&quot;</div>

H Schumacher