Informatics - Revision history

Jensflorian: /* Open source */ typo

2019-10-18T09:34:51Z

Open source: typo

← Older revision		Revision as of 09:34, 18 October 2019
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	[https://computationalpathologygroup.github.io/ASAP/ ASAP] is an open-source whole-slide image viewer.		[https://computationalpathologygroup.github.io/ASAP/ ASAP] is an open-source whole-slide image viewer.

	[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>		[https://www.ilastik.org/ Ilastik - interactive learning and segmentation toolkit] is an open source tool to perform segmentation and classification of images. Currently 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>

	==Health informatics directory==		==Health informatics directory==

Jensflorian: Update on open source and move of slide section to digital pathology

2019-10-16T14:00:12Z

Update on open source and move of slide section to digital pathology

← Older revision		Revision as of 14:00, 16 October 2019
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	[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>		[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>

	~~==Whole-Slide Images==~~
	*Most common formats:
	**Philips (.tiff)
	**Aperio (.svs, .tif)
	**Hamamatsu (.vms, .vmu, .ndpi)
	**Leica (.scn)
	**Sakura (.svslide)
	**MIRAX (.mrxs)
	**Ventana (.bif, .tif)
	**Generic tiled TIFF (.tif)
	[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>

	*There is a push for an open virtual slide format.

	*There is now a [http://dicom.nema.org/Dicom/DICOMWSI/ DICOM] standard for whole slide images.

	==Health informatics directory==		==Health informatics directory==

Jensflorian: /* Whole-Slide Images */ DICOM standard

2019-10-16T13:56:43Z

Whole-Slide Images: DICOM standard

← Older revision		Revision as of 13:56, 16 October 2019
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	**Ventana (.bif, .tif)		**Ventana (.bif, .tif)
	**Generic tiled TIFF (.tif)		**Generic tiled TIFF (.tif)
	[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>		[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>

	*There is a push for an open virtual slide format.		*There is a push for an open virtual slide format.
	*~~A free C library exists to read whole-slide images.<ref>URL:~~ [http://~~openslide~~.org/ ~~http:~~//~~openslide.org/~~]. ~~Accessed on: 3 May 2013.</ref>~~
			*There is now a [http://dicom.nema.org/Dicom/DICOMWSI/ DICOM] standard for whole slide images.

	==Health informatics directory==		==Health informatics directory==

Jensflorian: /* Open source */ Ilastik

2019-10-16T13:50:16Z

Open source: Ilastik

← Older revision		Revision as of 13:50, 16 October 2019
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	[https://computationalpathologygroup.github.io/ASAP/ ASAP] is an open-source whole-slide image viewer.		[https://computationalpathologygroup.github.io/ASAP/ ASAP] is an open-source whole-slide image viewer.

			[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>

	==Whole-Slide Images==		==Whole-Slide Images==

Jensflorian: /* Whole-Slide Images */ SlideJ for ImageJ

2019-10-16T13:38:03Z

Whole-Slide Images: SlideJ for ImageJ

← Older revision		Revision as of 13:38, 16 October 2019
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	**Ventana (.bif, .tif)		**Ventana (.bif, .tif)
	**Generic tiled TIFF (.tif)		**Generic tiled TIFF (.tif)
			[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>

	*There is a push for an open virtual slide format.		*There is a push for an open virtual slide format.
	*A free C library exists to read whole-slide images.<ref>URL: [http://openslide.org/ http://openslide.org/]. Accessed on: 3 May 2013.</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>

Jensflorian: /* Open source */ ASAP

2019-10-16T13:35:33Z

Open source: ASAP

← Older revision		Revision as of 13:35, 16 October 2019
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	[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>		[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>

	[https://medevel.com/cytomine-digital-pathology/ Cytomine] is a web-based open source image processing and analysis software.		[https://medevel.com/cytomine-digital-pathology/ Cytomine] is a web-based open source image processing and analysis software.

			[https://computationalpathologygroup.github.io/ASAP/ ASAP] is an open-source whole-slide image viewer.

	==Whole-Slide Images==		==Whole-Slide Images==

Jensflorian: /* Open source */ Cytomine

2019-10-16T13:32:39Z

Open source: Cytomine

← Older revision		Revision as of 13:32, 16 October 2019
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	[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>		[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>
			[https://medevel.com/cytomine-digital-pathology/ Cytomine] is a web-based open source image processing and analysis software.

	==Whole-Slide Images==		==Whole-Slide Images==

Jensflorian: /* Virtual slides */ Vendors

2019-10-16T13:30:25Z

Virtual slides: Vendors

← Older revision		Revision as of 13:30, 16 October 2019
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	[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>		[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>

	==~~Virtual slides~~==		==Whole-Slide Images==
			*Most common formats:
			**Philips (.tiff)
			**Aperio (.svs, .tif)
			**Hamamatsu (.vms, .vmu, .ndpi)
			**Leica (.scn)
			**Sakura (.svslide)
			**MIRAX (.mrxs)
			**Ventana (.bif, .tif)
			**Generic tiled TIFF (.tif)
	*There is a push for an open virtual slide format.		*There is a push for an open virtual slide format.
	*A free C library exists to read whole-slide images.<ref>URL: [http://openslide.org/ http://openslide.org/]. Accessed on: 3 May 2013.</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>

Jensflorian: /* Open source */ Qpath

2019-10-16T13:24:30Z

Open source: Qpath

← Older revision		Revision as of 13:24, 16 October 2019
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	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)].		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)].

			[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>

	==Virtual slides==		==Virtual slides==

Michael: /* Software in use at pathology departments */ +cytomine

2016-04-20T14:10:22Z

Software in use at pathology departments: +cytomine

← Older revision		Revision as of 14:10, 20 April 2016
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	===Biobanking management===		===Biobanking management===
	* Centraxx.		* Centraxx.

			===Image analysis===
			* 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>

	==Pathology wikis==		==Pathology wikis==