Hide last authors
| author | version | line-number | content |
|---|---|---|---|
 |
1.1 | 1 | (% class="jumbotron" %) |
| 2 | ((( | ||
| 3 | (% class="container" %) | ||
| 4 | ((( | ||
| |
9.1 | 5 | == (% style="color:#16a085" %)**QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images from Rodent Brain**(%%) == |
| 6 | |||
| 7 | (% style="color:#999999" %)Neural Systems Laboratory, University of Oslo | ||
| |
1.1 | 8 | ))) |
| 9 | ))) | ||
| 10 | |||
| |
9.1 | 11 | ==== ==== |
| |
7.1 | 12 | |
| |
8.1 | 13 | |
| |
13.1 | 14 | ==== (% style="color:#c0392b" %)**Workflow Description**(%%) ==== |
| |
1.1 | 15 | |
| |
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: |
| |
1.1 | 17 | |
| |
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. | ||
| |
1.1 | 21 | |
| |
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. |
| 23 | |||
| |
18.1 | 24 | Youtube video:[[ https:~~/~~/www.youtube.com/watch?v=yPkAbSfla_c>>https://www.youtube.com/watch?v=yPkAbSfla_c]] |
| |
14.1 | 25 | |
| |
16.1 | 26 | |
| |
14.1 | 27 | ==== (% style="color:#c0392b" %)**Workflow highlights**(%%) ==== |
| 28 | |||
| |
19.1 | 29 | - The QUINT workflow is semi-automated, combining three open-source software that can be operated without scripting knowledge. |
| |
15.1 | 30 | |
| 31 | ((( | ||
| |
19.1 | 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. |
| |
15.1 | 33 | |
| 34 | |||
| 35 | ==== (% style="color:#c0392b" %)**References**(%%) ==== | ||
| 36 | |||
| 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 | ||
| 38 | |||
| 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/]] | ||
| 40 | |||
| 41 | [[https:~~/~~/>>url:https://www.nitrc.org/projects/quicknii]][[www.nitrc.org/projects/quicknii>>url:https://www.nitrc.org/projects/quicknii]] | ||
| 42 | |||
| 43 | [[https:~~/~~/www.ilastik.org>>url:https://www.ilastik.org/]][[/>>url:https://www.ilastik.org/]] | ||
| |
14.1 | 44 | ))) |
| 45 | |||
| |
9.1 | 46 |