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paper.md

@@ -46,13 +46,13 @@ Additionally, we add a “background” threshold value which makes the action o
 Thresholdmann was coded in JavaScript and runs from a GitHub page. Code style was verified using ESLint ([https://eslint.org](https://eslint.org)). Unit tests and end-to-end tests were implemented using Mocha ([https://mochajs.org](https://mochajs.org)) and Puppeteer ([https://pptr.dev](https://pptr.dev)). Modifications in the code are continuously tested using CircleCI ([https://circleci.com](https://circleci.com)).
 
 # Figures
-![**Thresholdmann interface and 3D viewer.** The **left panel** allows to select different control point actions, set the thresholding direction, switch between the threshold mask or value view, open the 3D viewer, load or save the work, change the opacity of the mask, the brightness and contrast of the MRI, and information about the imaging data. The **central panel** is a stereotaxic viewer which allows the user to move through the slices using the slider at the bottom, to switch between the 3 stereotaxic planes, and to interactively set, move or remove control points. Users can view the threshold mask, or the corresponding threshold value space. The **right panel** shows for each control point the stereotaxic coordinates, an adjustment slider to change the local threshold, and the threshold value. The selected control point is highlighted in the panel and the viewer jumps to the corresponding slice. The **interactive 3D viewer** opens in a separate browser window.\label{fig:thresholdmann1}](https://raw.githubusercontent.com/neuroanatomy/thresholdmann/master/img/thresholdmann_fig1.png)
+![**Interface and 3D viewer.** The **left panel** allows to select different control point actions, set the thresholding direction, switch between the threshold mask or value view, open the 3D viewer, load or save the work, change the opacity of the mask, the brightness and contrast of the MRI, and information about the imaging data. The **central panel** is a stereotaxic viewer which allows the user to move through the slices using the slider at the bottom, to switch between the 3 stereotaxic planes, and to interactively set, move or remove control points. Users can view the threshold mask, or the corresponding threshold value space. The **right panel** shows for each control point the stereotaxic coordinates, an adjustment slider to change the local threshold, and the threshold value. The selected control point is highlighted in the panel and the viewer jumps to the corresponding slice. The **interactive 3D viewer** opens in a separate browser window.\label{fig:thresholdmann1}](https://raw.githubusercontent.com/neuroanatomy/thresholdmann/master/img/thresholdmann_fig1.png)
 
-![**Thresholdmann interface and workflow.** Control points (blue dots) are added by clicking at the desired position in the viewer. This adds a slider to the right, which can be used to locally adapt the threshold. The figure describes the progressive addition of control points to create a mask of the brain for a macaque from Prime-DE site "amu" [@Brochier_etal2019; @PrimeDE].\label{fig:thresholdmann2}](https://raw.githubusercontent.com/neuroanatomy/thresholdmann/master/img/thresholdmann_fig2.png)
+![**Usage example: Placing control points.** Control points (blue dots) are added by clicking at the desired position in the viewer. This adds a slider to the right, which can be used to locally adapt the threshold. The figure describes the progressive addition of control points to create a mask of the brain for a macaque from Prime-DE site "amu" [@Brochier_etal2019; @PrimeDE].\label{fig:thresholdmann2}](https://raw.githubusercontent.com/neuroanatomy/thresholdmann/master/img/thresholdmann_fig2.png)
 
-![**Thresholdmann viewer.** Threshold mask and corresponding threshold value. These volumes are updated in real time and can both be inspected interactively. The set of control points and the mask can be downloaded.\label{fig:thresholdmann3}](https://raw.githubusercontent.com/neuroanatomy/thresholdmann/master/img/thresholdmann_fig3.png)
+![**Usage example: Resulting mask and space-varying threshold.** Threshold mask and corresponding threshold value. These volumes are updated in real time and can both be inspected interactively. The set of control points and the mask can be downloaded.\label{fig:thresholdmann3}](https://raw.githubusercontent.com/neuroanatomy/thresholdmann/master/img/thresholdmann_fig3.png)
 
-![**Thresholdmann result.** We downloaded the mask presented above based on the shown set of eight control points. The brain region was sufficiently disjoint from the rest of the head so that a mathematical morphology closing was enough to completely separate it. The figure shows stereotaxic planes and a surface reconstruction of the mask.\label{fig:thresholdmann4}](https://raw.githubusercontent.com/neuroanatomy/thresholdmann/master/img/thresholdmann_fig4.png)
+![**Usage example: Final mask.** We downloaded the mask presented above based on the shown set of eight control points. The brain region was sufficiently disjoint from the rest of the head so that a mathematical morphology closing was enough to completely separate it. The figure shows stereotaxic planes and a surface reconstruction of the mask.\label{fig:thresholdmann4}](https://raw.githubusercontent.com/neuroanatomy/thresholdmann/master/img/thresholdmann_fig4.png)
 
 # Acknowledgements
 We thank Demian Wassermann for discussions about radial basis functions that inspired the first version of our tool. Funded by project DMOBE (ANR-21-CE45-0016) and the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No101033485 (KH Individual Fellowship).