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Verified Commit e93b96f4 authored by Marta Girona Alarcon's avatar Marta Girona Alarcon Committed by GitLab UZH
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......@@ -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"}
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