Last modified by puchades on 2022/11/02 10:16
From version 37.1
edited by puchades
on 2020/04/07 15:41
Change comment: There is no comment for this version
To version 46.1
edited by puchades
on 2020/09/23 13:42
Change comment: There is no comment for this version

Summary

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1 1  (% style="text-align:center" %)
2 -[[image:QUINT_workflow_pic.png||height="394" width="1011"]]
2 +[[image:QUINT_workflow_pic.png||height="391" width="1003"]]
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4 +
4 4  == (% style="color:#c0392b" %)**Workflow Description**(%%) ==
5 5  
6 6  The QUINT workflow facilitates the quantification and spatial analysis of labelled features in images of histological sections from the rodent brain using 3D reference atlases. The workflow is built on the following open access software:
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25 25  
26 -==== ====
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32 +QUINT workflow video
33 +
32 32  ==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ====
33 33  
34 -* The semi-automated QUINT workflow combines open access software that can be operated without scripting knowledge..
36 +* The semi-automated QUINT workflow uses open access software that can be operated without any scripting knowledge.
35 35  
36 36  (((
37 37  * 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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38 38  
39 39  ==== (% style="color:#c0392b" %)**References**(%%) ====
40 40  
41 -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
42 -
43 -[[https:~~/~~/www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]]
44 -
45 -[[https:~~/~~/www.nitrc.org/projects/quicknii>>https://www.nitrc.org/projects/quicknii]]
46 -
47 -[[https:~~/~~/www.nitrc.org/projects/visualign/>>url:https://www.nitrc.org/projects/visualign/]]
48 -
49 -[[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]]
43 +* 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]]
44 +* 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
45 +* [[Nutil>>https://github.com/Neural-Systems-at-UIO/nutil]]
46 +* [[QuickNII>>https://www.nitrc.org/projects/quicknii]]
47 +* [[VisuAlign>>https://www.nitrc.org/projects/visualign/]]
48 +* [[ilastik>>https://www.ilastik.org/]]
50 50  )))
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