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Last modified by puchades on 2022/11/02 10:16
From version 50.1
edited by puchades
on 2020/09/24 10:26
Change comment: There is no comment for this version
To version 58.1
edited by puchades
on 2020/10/05 10:17
Change comment: There is no comment for this version

Summary

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15 15  
16 16  In combination, the tools facilitate semi-automated quantification, eliminating the need for more time consuming methods such as stereological analysis with manual delineation of brain regions.
17 17  
18 -[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=yPkAbSfla_c]]
18 +[[[[image:Youtube_QUINT.PNG||height="282" style="float:left" width="500"]]>>https://www.youtube.com/watch?v=8oeg3qTzLnE]]
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33 33  
34 34  QUINT workflow video
35 35  
36 -==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
36 +== (% style="color:#c0392b" %)**Workflow highlights**(%%) ==
37 37  
38 -* The semi-automated QUINT workflow uses open access software that can be operated without any scripting knowledge.
38 +(% class="box successmessage" %)
39 +(((
40 +The semi-automated QUINT workflow uses open access software that can be operated without any scripting knowledge.
41 +)))
39 39  
40 40  (((
41 -* As the quantifications are performed in regions defined by a reference atlas, the region definitions are standardized, allowing comparisons of data from different laboratories.
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45 +(((
46 +As the quantifications are performed in regions defined by a reference atlas, the region definitions are standardized, allowing comparisons of data from different laboratories.
47 +)))
42 42  
43 43  ==== (% style="color:#c0392b" %)**References**(%%) ====
44 44  
45 -* Yates SC et al. 2019. QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Front. Neuroinform. 13:75. doi: [[10.3389/fninf.2019.00075>>https://www.frontiersin.org/articles/10.3389/fninf.2019.00075/full]]
46 -* Groeneboom NE, Yates SC, Puchades MA and Bjaalie JG (2020) Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. //Front. Neuroinform.// 14:37. doi: 10.3389/fninf.2020.00037
47 -* [[Nutil>>https://github.com/Neural-Systems-at-UIO/nutil]]
48 -* [[QuickNII>>https://www.nitrc.org/projects/quicknii]]
49 -* [[VisuAlign>>https://www.nitrc.org/projects/visualign/]]
50 -* [[ilastik>>https://www.ilastik.org/]]
51 +* Yates SC et al. (2019) QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Front. Neuroinform. 13:75. doi: [[10.3389/fninf.2019.00075>>https://www.frontiersin.org/articles/10.3389/fninf.2019.00075/full]]
52 +* Groeneboom NE, Yates SC, Puchades MA and Bjaalie JG (2020) Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. //Front. Neuroinform.// 14:37. doi: [[10.3389/fninf.2020.00037>>https://www.frontiersin.org/articles/10.3389/fninf.2020.00037/full]]
53 +* Berg S, Kutra D, Kroeger T, et al. & Kreshuk A (2019) ilastik: interactive machine learning for (bio)image analysis. Nat Methods. 16:1226-1232. doi: [[10.1038/s41592-019-0582-9>>https://www.nature.com/articles/s41592-019-0582-9]]
54 +* (((
55 +Puchades MA et al. (2019) Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PlosOne. 14(5): e0216796. doi: [[10.1371/journal.pone.0216796>>https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0216796]]
51 51  )))
57 +
58 +==== ====
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