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| 5 | == (% style="color:#16a085" %)**QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images from Rodent Brain**(%%) == | ||
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| 7 | (% style="color:#999999" %)Neural Systems Laboratory, University of Oslo | ||
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| 11 | ==== ==== | ||
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| 14 | ==== (% style="color:#c0392b" %)**Workflow Description**(%%) ==== | ||
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| 16 | The QUINT workflow enables the quantification and spatial analysis of labelled features in histological images of rodent brain sections based on reference atlases of the brain. It utilises three open-source software: | ||
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| 18 | 1. [[(% style="color:#2980b9" %)//ilastik//>>doc:.3\. Image segmentation with ilastik.WebHome]](%%) allows the extraction of labelled features such as cells by segmentation. | ||
| 19 | 1. [[(% style="color:#2980b9" %)//QuickNII//>>doc:.Image registration to reference atlas using QuickNII.WebHome]](%%) generates atlas maps customised to match the proportions and cutting plane of the brain sections. | ||
| 20 | 1. (% style="color:#2980b9" %)//Nutil//(%%) enables image [[transformations>>doc:.1\. Preparing the images.WebHome]], in addition to [[quantification and spatial analysis>>doc:.4\. Quantification and spatial analysis with Nutil.WebHome]] of features by drawing on the output of ilastik and QuickNII. | ||
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| 22 | 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. | ||
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| 24 | [[Youtube video>>https://www.youtube.com/watch?v=yPkAbSfla_c]] | ||
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| 26 | ==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ==== | ||
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| 28 | * The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge. | ||
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| 31 | * 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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| 33 | ==== (% style="color:#c0392b" %)**References**(%%) ==== | ||
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| 35 | 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 | ||
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| 37 | [[www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/quicknii]] | ||
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| 39 | www.nitrc.org/projects/quicknii | ||
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| 41 | [[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]] | ||
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