From e93b96f4c58cb76cfac3637d446db79bc56c8761 Mon Sep 17 00:00:00 2001
From: Marta Girona Alarcon <marta.gironaalarcon@uzh.ch>
Date: Wed, 18 Sep 2024 14:49:32 +0200
Subject: [PATCH] update

---
 .../Publication_page.qmd                        | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/webpage_contents/publications/20240901_Marta_GironaAlarcon/Publication_page.qmd b/webpage_contents/publications/20240901_Marta_GironaAlarcon/Publication_page.qmd
index 56e69c2..8483869 100644
--- a/webpage_contents/publications/20240901_Marta_GironaAlarcon/Publication_page.qmd
+++ b/webpage_contents/publications/20240901_Marta_GironaAlarcon/Publication_page.qmd
@@ -28,7 +28,7 @@ In this [DOI](https://doi.org/10.5281/zenodo.13773081), we provide full resoluti
 
 ### Pilot post mortem experiments
 In a previous beamtime (ESRF, 2020, December), *ex vivo* imaging was performed. The goal of the pilot experiments was to chose a contrast agent for the presented *in vivo* experiments. 
-The list of used contrast agents is available under the Zenodo download entry "tables_exVivo". We considered the Barium-based contrast agent (CA) to be the most promissing one and therefore decided to employ it for the *in vivo* experiments (Fig.  1). 
+The list of used contrast agents is available under the Zenodo download entry "tables_exVivo.7z". We considered the Barium-based contrast agent (CA) to be the most promissing one and therefore decided to employ it for the *in vivo* experiments (Fig.  1). 
 
 ![Fig.  1. Ex vivo coronal slices of three different mice injected with (left) Mouse.number 23, Gadolinium-based, (middle) Mouse.number 19, Barium-based and (right) Mouse.number 30, Gold-based contrast agent](images/post_mortem_overview.png)
 
@@ -51,24 +51,21 @@ Table 1. List of *ex vivo* mouse number, including the injected site and contras
 
 ### CSF spaces segmentation
 
-In the publication we have shown the need of infusing contrast agent 
-![](images/JP26-invivo-2scan-phase3-postinjection-brain-80-90min_web.png){width="600"}
+In the publication, we have shown the need of infusing contrast agent to achieve a semi-automatic segmentation. Here, we show a rendering of one segmentation. In the downloads, we have provided a segmentation of a timeseries imaging in the brain ventricles, which can be found under "videos_Reconstructions.7z".
 
-![Fig.  2. Three dimensional rendering of CSF spaces enclosed in the mouse skull: Infusion of contrast agent in the lateral ventricles during high-resolution synchrotron radiation-based hard X-ray computed tomography imaging allows 3D visualization with virtual slicing in all directions. Lateral ventricles in blue, third ventricle in green, aqueduct in pink and fourth ventricle in yellow.]
+
+![Fig.  2. Three dimensional rendering of CSF spaces enclosed in the mouse skull: Infusion of contrast agent in the lateral ventricles during high-resolution synchrotron radiation-based hard X-ray computed tomography imaging allows 3D visualization with virtual slicing in all directions. Lateral ventricles in blue, third ventricle in green, aqueduct in pink and fourth ventricle in yellow.](images/JP26-invivo-2scan-phase3-postinjection-brain-80-90min_web.png){width="600"}
 
 
 ## Additional materials
 We have additively manufactured the mouse holder, optimized for vertical imaging while ensuring fixation of the mouse skull. 
-![](images/holder_1.jpeg)
-
-![Fig.  3. Visualization of the mouse holder mounted on the imaging rotational stage.]
+![Fig.  3. Visualization of the mouse holder mounted on the imaging rotational stage.](images/holder_1.jpeg)
 
-![](images/holder_2_holes.jpeg){width="300"}
 
-![Fig.  4. Transparent visualization of body mouse holder part containing the water channels to ensure physiological temperature of the mouse.]
+![Fig.  4. Transparent visualization of body mouse holder part containing the water channels to ensure physiological temperature of the mouse.](images/holder_2_holes.jpeg){width="300"}
 
 Additionally, we assambled a customized mouse stage for two surgical procedures: tracheotomy and cisterna magna infusion (Fig.  ).
-![](images/cisternamagna_stage.jpeg){width="450"}
+![Fig.  5. Customized tracheotomy and cisterna magna stage. Available as a 3D model in the downloads.](images/cisternamagna_stage.jpeg){width="450"}
 
 
 
-- 
GitLab