https://librepathology.org/w/index.php?title=Informatics&feed=atom&action=history
Informatics - Revision history
2024-03-29T09:39:00Z
Revision history for this page on the wiki
MediaWiki 1.36.3
https://librepathology.org/w/index.php?title=Informatics&diff=50449&oldid=prev
Jensflorian: /* Open source */ typo
2019-10-18T09:34:51Z
<p><span dir="auto"><span class="autocomment">Open source: </span> typo</span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 09:34, 18 October 2019</td>
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<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>[https://computationalpathologygroup.github.io/ASAP/ ASAP] is an open-source whole-slide image viewer.</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>[https://computationalpathologygroup.github.io/ASAP/ ASAP] is an open-source whole-slide image viewer.</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;"><br/></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;"><br/></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[https://www.ilastik.org/ Ilastik - interactive learning and segmentation toolkit] is an open source tool to perform segmentation and classification of images. <del style="font-weight: bold; text-decoration: none;">Cureently </del>it does not support full virtual slides.<ref>{{Cite journal | last1 = Berg | first1 = S. | last2 = Kutra | first2 = D. | last3 = Kroeger | first3 = T. | last4 = Straehle | first4 = CN. | last5 = Kausler | first5 = BX. | last6 = Haubold | first6 = C. | last7 = Schiegg | first7 = M. | last8 = Ales | first8 = J. | last9 = Beier | first9 = T. | title = ilastik: interactive machine learning for (bio)image analysis. | journal = Nat Methods | volume = | issue = | pages = | month = Sep | year = 2019 | doi = 10.1038/s41592-019-0582-9 | PMID = 31570887 }}</ref></div></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>[https://www.ilastik.org/ Ilastik - interactive learning and segmentation toolkit] is an open source tool to perform segmentation and classification of images. <ins style="font-weight: bold; text-decoration: none;">Currently </ins>it does not support full virtual slides.<ref>{{Cite journal | last1 = Berg | first1 = S. | last2 = Kutra | first2 = D. | last3 = Kroeger | first3 = T. | last4 = Straehle | first4 = CN. | last5 = Kausler | first5 = BX. | last6 = Haubold | first6 = C. | last7 = Schiegg | first7 = M. | last8 = Ales | first8 = J. | last9 = Beier | first9 = T. | title = ilastik: interactive machine learning for (bio)image analysis. | journal = Nat Methods | volume = | issue = | pages = | month = Sep | year = 2019 | doi = 10.1038/s41592-019-0582-9 | PMID = 31570887 }}</ref></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;"><br/></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;"><br/></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>==Health informatics directory==</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>==Health informatics directory==</div></td></tr>
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Jensflorian
https://librepathology.org/w/index.php?title=Informatics&diff=50430&oldid=prev
Jensflorian: Update on open source and move of slide section to digital pathology
2019-10-16T14:00:12Z
<p>Update on open source and move of slide section to digital pathology</p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<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 14:00, 16 October 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l42">Line 42:</td>
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<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;"><br/></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;"><br/></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>[https://www.ilastik.org/ Ilastik - interactive learning and segmentation toolkit] is an open source tool to perform segmentation and classification of images. Cureently it does not support full virtual slides.<ref>{{Cite journal | last1 = Berg | first1 = S. | last2 = Kutra | first2 = D. | last3 = Kroeger | first3 = T. | last4 = Straehle | first4 = CN. | last5 = Kausler | first5 = BX. | last6 = Haubold | first6 = C. | last7 = Schiegg | first7 = M. | last8 = Ales | first8 = J. | last9 = Beier | first9 = T. | title = ilastik: interactive machine learning for (bio)image analysis. | journal = Nat Methods | volume = | issue = | pages = | month = Sep | year = 2019 | doi = 10.1038/s41592-019-0582-9 | PMID = 31570887 }}</ref></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>[https://www.ilastik.org/ Ilastik - interactive learning and segmentation toolkit] is an open source tool to perform segmentation and classification of images. Cureently it does not support full virtual slides.<ref>{{Cite journal | last1 = Berg | first1 = S. | last2 = Kutra | first2 = D. | last3 = Kroeger | first3 = T. | last4 = Straehle | first4 = CN. | last5 = Kausler | first5 = BX. | last6 = Haubold | first6 = C. | last7 = Schiegg | first7 = M. | last8 = Ales | first8 = J. | last9 = Beier | first9 = T. | title = ilastik: interactive machine learning for (bio)image analysis. | journal = Nat Methods | volume = | issue = | pages = | month = Sep | year = 2019 | doi = 10.1038/s41592-019-0582-9 | PMID = 31570887 }}</ref></div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">==Whole-Slide Images==</del></div></td><td colspan="2"></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">*Most common formats:</del></div></td><td colspan="2"></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"> **Philips (.tiff)</del></div></td><td colspan="2"></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"> **Aperio (.svs, .tif)</del></div></td><td colspan="2"></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"> **Hamamatsu (.vms, .vmu, .ndpi)</del></div></td><td colspan="2"></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"> **Leica (.scn)</del></div></td><td colspan="2"></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"> **Sakura (.svslide)</del></div></td><td colspan="2"></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"> **MIRAX (.mrxs)</del></div></td><td colspan="2"></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"> **Ventana (.bif, .tif)</del></div></td><td colspan="2"></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"> **Generic tiled TIFF (.tif)</del></div></td><td colspan="2"></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">[https://imagej.net/SlideJ SlideJ] is a plugin for ImageJ for viewing most of the above mentioned formats.<ref>{{Cite journal | last1 = Della Mea | first1 = V. | last2 = Baroni | first2 = GL. | last3 = Pilutti | first3 = D. | last4 = Di Loreto | first4 = C. | title = SlideJ: An ImageJ plugin for automated processing of whole slide images. | journal = PLoS One | volume = 12 | issue = 7 | pages = e0180540 | month = | year = 2017 | doi = 10.1371/journal.pone.0180540 | PMID = 28683129 }}</ref> A free C library exists to read whole-slide images.<ref>URL: [http://openslide.org/ http://openslide.org/]. Accessed on: 3 May 2013.</ref></del></div></td><td colspan="2"></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"> </del></div></td><td colspan="2"></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">*There is a push for an open virtual slide format.</del></div></td><td colspan="2"></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">*There is now a [http://dicom.nema.org/Dicom/DICOMWSI/ DICOM] standard for whole slide images.</del></div></td><td colspan="2"></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;"><br/></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;"><br/></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>==Health informatics directory==</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>==Health informatics directory==</div></td></tr>
</table>
Jensflorian
https://librepathology.org/w/index.php?title=Informatics&diff=50428&oldid=prev
Jensflorian: /* Whole-Slide Images */ DICOM standard
2019-10-16T13:56:43Z
<p><span dir="auto"><span class="autocomment">Whole-Slide Images: </span> DICOM standard</span></p>
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<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 13:56, 16 October 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l53">Line 53:</td>
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<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> **Ventana (.bif, .tif)</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> **Ventana (.bif, .tif)</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> **Generic tiled TIFF (.tif)</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> **Generic tiled TIFF (.tif)</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[https://imagej.net/SlideJ SlideJ] is a plugin for ImageJ for viewing most of the above mentioned formats.<ref>{{Cite journal | last1 = Della Mea | first1 = V. | last2 = Baroni | first2 = GL. | last3 = Pilutti | first3 = D. | last4 = Di Loreto | first4 = C. | title = SlideJ: An ImageJ plugin for automated processing of whole slide images. | journal = PLoS One | volume = 12 | issue = 7 | pages = e0180540 | month = | year = 2017 | doi = 10.1371/journal.pone.0180540 | PMID = 28683129 }}</ref></div></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>[https://imagej.net/SlideJ SlideJ] is a plugin for ImageJ for viewing most of the above mentioned formats.<ref>{{Cite journal | last1 = Della Mea | first1 = V. | last2 = Baroni | first2 = GL. | last3 = Pilutti | first3 = D. | last4 = Di Loreto | first4 = C. | title = SlideJ: An ImageJ plugin for automated processing of whole slide images. | journal = PLoS One | volume = 12 | issue = 7 | pages = e0180540 | month = | year = 2017 | doi = 10.1371/journal.pone.0180540 | PMID = 28683129 }}<ins style="font-weight: bold; text-decoration: none;"></ref> A free C library exists to read whole-slide images.<ref>URL: [http://openslide.org/ http://openslide.org/]. Accessed on: 3 May 2013.</ins></ref></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> </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> </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>*There is a push for an open virtual slide format.</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>*There is a push for an open virtual slide format.</div></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*<del style="font-weight: bold; text-decoration: none;">A free C library exists to read whole-slide images.<ref>URL: </del>[http://<del style="font-weight: bold; text-decoration: none;">openslide</del>.org/ <del style="font-weight: bold; text-decoration: none;">http:</del>//<del style="font-weight: bold; text-decoration: none;">openslide.org/</del>]. <del style="font-weight: bold; text-decoration: none;">Accessed on: 3 May 2013.</ref></del></div></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> </div></td></tr>
<tr><td colspan="2"></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>*<ins style="font-weight: bold; text-decoration: none;">There is now a </ins>[http://<ins style="font-weight: bold; text-decoration: none;">dicom.nema</ins>.org/<ins style="font-weight: bold; text-decoration: none;">Dicom</ins>/<ins style="font-weight: bold; text-decoration: none;">DICOMWSI</ins>/ <ins style="font-weight: bold; text-decoration: none;">DICOM</ins>] <ins style="font-weight: bold; text-decoration: none;">standard for whole slide images</ins>.</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;"><br/></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;"><br/></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>==Health informatics directory==</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>==Health informatics directory==</div></td></tr>
</table>
Jensflorian
https://librepathology.org/w/index.php?title=Informatics&diff=50427&oldid=prev
Jensflorian: /* Open source */ Ilastik
2019-10-16T13:50:16Z
<p><span dir="auto"><span class="autocomment">Open source: </span> Ilastik</span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 13:50, 16 October 2019</td>
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<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;"><br/></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;"><br/></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>[https://computationalpathologygroup.github.io/ASAP/ ASAP] is an open-source whole-slide image viewer.</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>[https://computationalpathologygroup.github.io/ASAP/ ASAP] is an open-source whole-slide image viewer.</div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;">[https://www.ilastik.org/ Ilastik - interactive learning and segmentation toolkit] is an open source tool to perform segmentation and classification of images. Cureently it does not support full virtual slides.<ref>{{Cite journal | last1 = Berg | first1 = S. | last2 = Kutra | first2 = D. | last3 = Kroeger | first3 = T. | last4 = Straehle | first4 = CN. | last5 = Kausler | first5 = BX. | last6 = Haubold | first6 = C. | last7 = Schiegg | first7 = M. | last8 = Ales | first8 = J. | last9 = Beier | first9 = T. | title = ilastik: interactive machine learning for (bio)image analysis. | journal = Nat Methods | volume = | issue = | pages = | month = Sep | year = 2019 | doi = 10.1038/s41592-019-0582-9 | PMID = 31570887 }}</ref></ins></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;"><br/></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;"><br/></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>==Whole-Slide Images==</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>==Whole-Slide Images==</div></td></tr>
</table>
Jensflorian
https://librepathology.org/w/index.php?title=Informatics&diff=50426&oldid=prev
Jensflorian: /* Whole-Slide Images */ SlideJ for ImageJ
2019-10-16T13:38:03Z
<p><span dir="auto"><span class="autocomment">Whole-Slide Images: </span> SlideJ for ImageJ</span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 13:38, 16 October 2019</td>
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<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> **Generic tiled TIFF (.tif)</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> **Generic tiled TIFF (.tif)</div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;">[https://imagej.net/SlideJ SlideJ] is a plugin for ImageJ for viewing most of the above mentioned formats.<ref>{{Cite journal | last1 = Della Mea | first1 = V. | last2 = Baroni | first2 = GL. | last3 = Pilutti | first3 = D. | last4 = Di Loreto | first4 = C. | title = SlideJ: An ImageJ plugin for automated processing of whole slide images. | journal = PLoS One | volume = 12 | issue = 7 | pages = e0180540 | month = | year = 2017 | doi = 10.1371/journal.pone.0180540 | PMID = 28683129 }}</ref></ins></div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;"> </ins></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>*There is a push for an open virtual slide format.</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>*There is a push for an open virtual slide format.</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>*A free C library exists to read whole-slide images.<ref>URL: [http://openslide.org/ http://openslide.org/]. Accessed on: 3 May 2013.</ref></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>*A free C library exists to read whole-slide images.<ref>URL: [http://openslide.org/ http://openslide.org/]. Accessed on: 3 May 2013.</ref></div></td></tr>
</table>
Jensflorian
https://librepathology.org/w/index.php?title=Informatics&diff=50425&oldid=prev
Jensflorian: /* Open source */ ASAP
2019-10-16T13:35:33Z
<p><span dir="auto"><span class="autocomment">Open source: </span> ASAP</span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 13:35, 16 October 2019</td>
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<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;"><br/></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;"><br/></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>[https://qupath.github.io/ QPath] is a open source software platform for whole slide image analysis.<ref>{{Cite journal | last1 = Bankhead | first1 = P. | last2 = Loughrey | first2 = MB. | last3 = Fernández | first3 = JA. | last4 = Dombrowski | first4 = Y. | last5 = McArt | first5 = DG. | last6 = Dunne | first6 = PD. | last7 = McQuaid | first7 = S. | last8 = Gray | first8 = RT. | last9 = Murray | first9 = LJ. | title = QuPath: Open source software for digital pathology image analysis. | journal = Sci Rep | volume = 7 | issue = 1 | pages = 16878 | month = 12 | year = 2017 | doi = 10.1038/s41598-017-17204-5 | PMID = 29203879 }}</ref></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>[https://qupath.github.io/ QPath] is a open source software platform for whole slide image analysis.<ref>{{Cite journal | last1 = Bankhead | first1 = P. | last2 = Loughrey | first2 = MB. | last3 = Fernández | first3 = JA. | last4 = Dombrowski | first4 = Y. | last5 = McArt | first5 = DG. | last6 = Dunne | first6 = PD. | last7 = McQuaid | first7 = S. | last8 = Gray | first8 = RT. | last9 = Murray | first9 = LJ. | title = QuPath: Open source software for digital pathology image analysis. | journal = Sci Rep | volume = 7 | issue = 1 | pages = 16878 | month = 12 | year = 2017 | doi = 10.1038/s41598-017-17204-5 | PMID = 29203879 }}</ref></div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;"></ins></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>[https://medevel.com/cytomine-digital-pathology/ Cytomine] is a web-based open source image processing and analysis software.</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>[https://medevel.com/cytomine-digital-pathology/ Cytomine] is a web-based open source image processing and analysis software.</div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;">[https://computationalpathologygroup.github.io/ASAP/ ASAP] is an open-source whole-slide image viewer.</ins></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;"><br/></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;"><br/></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>==Whole-Slide Images==</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>==Whole-Slide Images==</div></td></tr>
</table>
Jensflorian
https://librepathology.org/w/index.php?title=Informatics&diff=50424&oldid=prev
Jensflorian: /* Open source */ Cytomine
2019-10-16T13:32:39Z
<p><span dir="auto"><span class="autocomment">Open source: </span> Cytomine</span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 13:32, 16 October 2019</td>
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<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;"><br/></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;"><br/></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>[https://qupath.github.io/ QPath] is a open source software platform for whole slide image analysis.<ref>{{Cite journal | last1 = Bankhead | first1 = P. | last2 = Loughrey | first2 = MB. | last3 = Fernández | first3 = JA. | last4 = Dombrowski | first4 = Y. | last5 = McArt | first5 = DG. | last6 = Dunne | first6 = PD. | last7 = McQuaid | first7 = S. | last8 = Gray | first8 = RT. | last9 = Murray | first9 = LJ. | title = QuPath: Open source software for digital pathology image analysis. | journal = Sci Rep | volume = 7 | issue = 1 | pages = 16878 | month = 12 | year = 2017 | doi = 10.1038/s41598-017-17204-5 | PMID = 29203879 }}</ref></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>[https://qupath.github.io/ QPath] is a open source software platform for whole slide image analysis.<ref>{{Cite journal | last1 = Bankhead | first1 = P. | last2 = Loughrey | first2 = MB. | last3 = Fernández | first3 = JA. | last4 = Dombrowski | first4 = Y. | last5 = McArt | first5 = DG. | last6 = Dunne | first6 = PD. | last7 = McQuaid | first7 = S. | last8 = Gray | first8 = RT. | last9 = Murray | first9 = LJ. | title = QuPath: Open source software for digital pathology image analysis. | journal = Sci Rep | volume = 7 | issue = 1 | pages = 16878 | month = 12 | year = 2017 | doi = 10.1038/s41598-017-17204-5 | PMID = 29203879 }}</ref></div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;">[https://medevel.com/cytomine-digital-pathology/ Cytomine] is a web-based open source image processing and analysis software.</ins></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;"><br/></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;"><br/></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>==Whole-Slide Images==</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>==Whole-Slide Images==</div></td></tr>
</table>
Jensflorian
https://librepathology.org/w/index.php?title=Informatics&diff=50423&oldid=prev
Jensflorian: /* Virtual slides */ Vendors
2019-10-16T13:30:25Z
<p><span dir="auto"><span class="autocomment">Virtual slides: </span> Vendors</span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 13:30, 16 October 2019</td>
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<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>[https://qupath.github.io/ QPath] is a open source software platform for whole slide image analysis.<ref>{{Cite journal | last1 = Bankhead | first1 = P. | last2 = Loughrey | first2 = MB. | last3 = Fernández | first3 = JA. | last4 = Dombrowski | first4 = Y. | last5 = McArt | first5 = DG. | last6 = Dunne | first6 = PD. | last7 = McQuaid | first7 = S. | last8 = Gray | first8 = RT. | last9 = Murray | first9 = LJ. | title = QuPath: Open source software for digital pathology image analysis. | journal = Sci Rep | volume = 7 | issue = 1 | pages = 16878 | month = 12 | year = 2017 | doi = 10.1038/s41598-017-17204-5 | PMID = 29203879 }}</ref></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>[https://qupath.github.io/ QPath] is a open source software platform for whole slide image analysis.<ref>{{Cite journal | last1 = Bankhead | first1 = P. | last2 = Loughrey | first2 = MB. | last3 = Fernández | first3 = JA. | last4 = Dombrowski | first4 = Y. | last5 = McArt | first5 = DG. | last6 = Dunne | first6 = PD. | last7 = McQuaid | first7 = S. | last8 = Gray | first8 = RT. | last9 = Murray | first9 = LJ. | title = QuPath: Open source software for digital pathology image analysis. | journal = Sci Rep | volume = 7 | issue = 1 | pages = 16878 | month = 12 | year = 2017 | doi = 10.1038/s41598-017-17204-5 | PMID = 29203879 }}</ref></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;"><br/></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;"><br/></td></tr>
<tr><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: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>==<del style="font-weight: bold; text-decoration: none;">Virtual slides</del>==</div></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>==<ins style="font-weight: bold; text-decoration: none;">Whole-Slide Images</ins>==</div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;">*Most common formats:</ins></div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;"> **Philips (.tiff)</ins></div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;"> **Aperio (.svs, .tif)</ins></div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;"> **Hamamatsu (.vms, .vmu, .ndpi)</ins></div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;"> **Leica (.scn)</ins></div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;"> **Sakura (.svslide)</ins></div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;"> **MIRAX (.mrxs)</ins></div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;"> **Ventana (.bif, .tif)</ins></div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;"> **Generic tiled TIFF (.tif)</ins></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>*There is a push for an open virtual slide format.</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>*There is a push for an open virtual slide format.</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>*A free C library exists to read whole-slide images.<ref>URL: [http://openslide.org/ http://openslide.org/]. Accessed on: 3 May 2013.</ref></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>*A free C library exists to read whole-slide images.<ref>URL: [http://openslide.org/ http://openslide.org/]. Accessed on: 3 May 2013.</ref></div></td></tr>
</table>
Jensflorian
https://librepathology.org/w/index.php?title=Informatics&diff=50422&oldid=prev
Jensflorian: /* Open source */ Qpath
2019-10-16T13:24:30Z
<p><span dir="auto"><span class="autocomment">Open source: </span> Qpath</span></p>
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<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 13:24, 16 October 2019</td>
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<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;"><br/></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;"><br/></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>A few institutions (mostly American) are coming to understand this and have formed the [http://www.opendp.org/ Open Digital Pathology Consortium (opendp.org)]. There is also an [http://openslide.org/ open slide project (openslide.org)].</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>A few institutions (mostly American) are coming to understand this and have formed the [http://www.opendp.org/ Open Digital Pathology Consortium (opendp.org)]. There is also an [http://openslide.org/ open slide project (openslide.org)].</div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;">[https://qupath.github.io/ QPath] is a open source software platform for whole slide image analysis.<ref>{{Cite journal | last1 = Bankhead | first1 = P. | last2 = Loughrey | first2 = MB. | last3 = Fernández | first3 = JA. | last4 = Dombrowski | first4 = Y. | last5 = McArt | first5 = DG. | last6 = Dunne | first6 = PD. | last7 = McQuaid | first7 = S. | last8 = Gray | first8 = RT. | last9 = Murray | first9 = LJ. | title = QuPath: Open source software for digital pathology image analysis. | journal = Sci Rep | volume = 7 | issue = 1 | pages = 16878 | month = 12 | year = 2017 | doi = 10.1038/s41598-017-17204-5 | PMID = 29203879 }}</ref></ins></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;"><br/></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;"><br/></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>==Virtual slides==</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>==Virtual slides==</div></td></tr>
</table>
Jensflorian
https://librepathology.org/w/index.php?title=Informatics&diff=43810&oldid=prev
Michael: /* Software in use at pathology departments */ +cytomine
2016-04-20T14:10:22Z
<p><span dir="auto"><span class="autocomment">Software in use at pathology departments: </span> +cytomine</span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 14:10, 20 April 2016</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l19">Line 19:</td>
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<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>===Biobanking management===</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>===Biobanking management===</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>* Centraxx.</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>* Centraxx.</div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;">===Image analysis===</ins></div></td></tr>
<tr><td colspan="2"></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><ins style="font-weight: bold; text-decoration: none;">* Cytomine - under an ''Apache license''.<ref>URL: [http://www.cytomine.be/ http://www.cytomine.be/]. Accessed on: 20 April 2016.</ref><ref name=pmid26755625>{{Cite journal | last1 = Marée | first1 = R. | last2 = Rollus | first2 = L. | last3 = Stévens | first3 = B. | last4 = Hoyoux | first4 = R. | last5 = Louppe | first5 = G. | last6 = Vandaele | first6 = R. | last7 = Begon | first7 = JM. | last8 = Kainz | first8 = P. | last9 = Geurts | first9 = P. | title = Collaborative analysis of multi-gigapixel imaging data using Cytomine. | journal = Bioinformatics | volume = | issue = | pages = | month = Jan | year = 2016 | doi = 10.1093/bioinformatics/btw013 | PMID = 26755625 }}</ref></ins></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;"><br/></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;"><br/></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>==Pathology wikis==</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>==Pathology wikis==</div></td></tr>
</table>
Michael