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9.1 | 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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9.1 | 11 | ==== ==== |
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13.1 | 14 | ==== (% style="color:#c0392b" %)**Workflow Description**(%%) ==== |
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9.1 | 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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12.1 | 18 | 1. (% style="color:#2980b9" %)//ilastik//(%%) allows the extraction of labelled features such as cells by segmentation. |
| 19 | 1. (% style="color:#2980b9" %)//QuickNII//(%%) generates atlas maps customised to match the proportions and cutting plane of the brain sections. | ||
| 20 | 1. (% style="color:#2980b9" %)//Nutil//(%%) enables image transformations, in addition to quantification and spatial analysis of features by drawing on the output of ilastik and QuickNII. | ||
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9.1 | 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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17.1 | 24 | Youtube video[[ https:~~/~~/www.youtube.com/watch?v=yPkAbSfla_c>>https://www.youtube.com/watch?v=yPkAbSfla_c]] |
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14.1 | 27 | ==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ==== |
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| 29 | * The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge. | ||
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14.1 | 32 | 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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| 35 | ==== (% style="color:#c0392b" %)**References**(%%) ==== | ||
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| 37 | 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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| 39 | [[https>>url:https://www.nitrc.org/projects/nutil/]][[:~~/~~/www.nitrc.org/projects/nutil>>url:https://www.nitrc.org/projects/nutil/]][[/>>url:https://www.nitrc.org/projects/nutil/]] | ||
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| 41 | [[https:~~/~~/>>url:https://www.nitrc.org/projects/quicknii]][[www.nitrc.org/projects/quicknii>>url:https://www.nitrc.org/projects/quicknii]] | ||
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| 43 | [[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]] | ||
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