Attention: The Collaboratory IAM will down for up to 1 hour on Monday, the 7th of July 2025 starting from 5pm CEST (my timezone) for up to 1 hour. Any and all services, which require a user login with an EBRAINS account, will be un-available during that time


Last modified by puchades on 2022/11/02 10:16
From version 58.1
edited by puchades
on 2020/10/05 10:17
Change comment: There is no comment for this version
To version 53.1
edited by puchades
on 2020/09/24 11:36
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -35,25 +35,17 @@
35 35  
36 36  == (% style="color:#c0392b" %)**Workflow highlights**(%%) ==
37 37  
38 -(% class="box successmessage" %)
39 -(((
40 -The semi-automated QUINT workflow uses open access software that can be operated without any scripting knowledge.
41 -)))
38 +* The semi-automated QUINT workflow uses open access software that can be operated without any scripting knowledge.
42 42  
43 43  (((
44 -(% class="box successmessage" %)
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 -)))
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.
48 48  
49 49  ==== (% style="color:#c0392b" %)**References**(%%) ====
50 50  
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]]
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/]]
56 56  )))
57 -
58 -==== ====
59 -)))