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Speedup deployement #640

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May 25, 2023
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Speedup deployement #640

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73e428e
PW38_2023_GranCanaria/Projects/SlicerLiver: Remove duplicated webm files
jcfr May 25, 2023
99eecbc
(PW37|PW38)/SlicerLiver: Fix links in "Background and References" sec…
jcfr May 25, 2023
b69960e
PW37/SlicerLiver: Move webm files as ProjectWeekResources release assets
jcfr May 25, 2023
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PW35/US_CT_VertebraRegistration: Move gif file as ProjectWeekResource…
jcfr May 25, 2023
f14b705
PW38_2023_GranCanaria/Projects/SlicerLiver: Remove duplicated mp4 files
jcfr May 25, 2023
2b422fd
PW37/SlicerLiver: Move mp4 files as ProjectWeekResources release assets
jcfr May 25, 2023
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Update projects referencing media from ProjectWeekResources release a…
jcfr May 25, 2023
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Binary file removed ...2019_GranCanaria/Projects/Data-glove_for_virtual_operations/20190201_095221.gif
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2 changes: 1 addition & 1 deletion PW30_2019_GranCanaria/Projects/Data-glove_for_virtual_operations/README.md
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Expand Up @@ -46,7 +46,7 @@ We built a data-glove that tracks hand movements. Our goal is to connect it to S

Result:

![Result](20190201_095221.gif)
![Result](https://github.com/NA-MIC/ProjectWeek/releases/download/project-week-resources/PW30__Data-glove_for_virtual_operations__20190201_095221.gif)

# Background and References

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4 changes: 2 additions & 2 deletions PW35_2021_Virtual/Projects/US_CT_VertebraRegistration/README.md
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Expand Up @@ -51,7 +51,7 @@ The goal is to combine the registration method for _open_ surgery implemented in

**Generate aligned CT-US data:**

![US-CT Data](US-CTAlignment.gif)
![US-CT Data](https://github.com/NA-MIC/ProjectWeek/releases/download/project-week-resources/PW35__US_CT_VertebraRegistration__US-CTAlignment.gif)



Expand All @@ -67,4 +67,4 @@ The goal is to combine the registration method for _open_ surgery implemented in

# Background and References

<!-- If you developed any software, include link to the source code repository. If possible, also add links to sample data, and to any relevant publications. -->
<!-- If you developed any software, include link to the source code repository. If possible, also add links to sample data, and to any relevant publications. -->
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2 changes: 1 addition & 1 deletion PW36_2022_Virtual/Projects/TMRCatheterNavigation/README.md
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Expand Up @@ -48,7 +48,7 @@ A vessel model will be reconstructed from a preoperative 3D CT. During the opera

![Experimental setup](img1.png)
![Experimental setup](img2.png)
![Experimental setup](video.gif)
![Experimental setup](https://github.com/NA-MIC/ProjectWeek/releases/download/project-week-resources/PW36__TMRCatheterNavigation__video.gif)

# Background and References

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29 changes: 26 additions & 3 deletions PW37_2022_Virtual/Projects/SlicerLiver/README.md
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Expand Up @@ -54,6 +54,30 @@ PW36](https://github.com/NA-MIC/ProjectWeek/tree/master/PW36_2022_Virtual/Projec

<img src="https://github.com/ALive-research/Slicer-Liver/blob/master/Screenshots/Slicer-Liver_screenshot_08.png?raw=true" width="50%">

<video controls width="250">
<source src="https://github.com/NA-MIC/ProjectWeek/releases/download/project-week-resources/PW37__SlicerLiver__liver_resection.mp4" type="video/webm">
Download
<a href="https://github.com/NA-MIC/ProjectWeek/releases/download/project-week-resources/PW37__SlicerLiver__liver_resection.mp4">PW37__SlicerLiver__liver_resection.mp4</a>
</video>

<video controls width="250">
<source src="https://github.com/NA-MIC/ProjectWeek/releases/download/project-week-resources/PW37__SlicerLiver__distance-tumor.webm" type="video/webm">
Download
<a href="https://github.com/NA-MIC/ProjectWeek/releases/download/project-week-resources/PW37__SlicerLiver__distance-tumor.webm">PW37__SlicerLiver__distance-tumor.webm</a>
</video>

<video controls width="250">
<source src="https://github.com/NA-MIC/ProjectWeek/releases/download/project-week-resources/PW37__SlicerLiver__distance-vessels.webm" type="video/webm">
Download
<a href="https://github.com/NA-MIC/ProjectWeek/releases/download/project-week-resources/PW37__SlicerLiver__distance-vessels.webm">PW37__SlicerLiver__distance-vessels.webm</a>
</video>

<video controls width="250">
<source src="https://github.com/NA-MIC/ProjectWeek/releases/download/project-week-resources/PW37__SlicerLiver__planning.webm" type="video/webm">
Download
<a href="https://github.com/NA-MIC/ProjectWeek/releases/download/project-week-resources/PW37__SlicerLiver__planning.webm">PW37__SlicerLiver__planning.webm</a>
</video>

## Progress and Next Steps

In this project week, we have changed the user interaction to use segmentations instead of models, which greatly simplifies the user interaction.
Expand All @@ -63,9 +87,8 @@ There is a PR for adding this extension to the extension manager. This be effect
There are still standard features (e.g., volumetry computation) and new research features (e.g, risk maps visualization, new planning algorithms) that we would like to implement in future Project Weeks.

# Background and References
1. [Slicer-Liver PW36](https://github.com/NA-MIC/ProjectWeek/tree/master/PW36_2022_Virtual/Projects/Slicer-Liver
1. [Slicer-Liver PW35](https://github.com/NA-MIC/ProjectWeek/tree/master/PW35_2021_Virtual/Projects/Slicer-Liver
"Slicer-Liver in the last ProjectWeek") (June 2021)
1. [Slicer-Liver PW36](https://github.com/NA-MIC/ProjectWeek/tree/master/PW36_2022_Virtual/Projects/Slicer-Liver) (January 2022)
1. [Slicer-Liver PW35](https://github.com/NA-MIC/ProjectWeek/tree/master/PW35_2021_Virtual/Projects/Slicer-Liver) (June 2021)
1. [NorMIT-Plan at NA-MIC project week](https://projectweek.na-mic.org/PW33_2020_GranCanaria/Projects/NorMIT-Plan/) (january 2020)
1. [NorMIT-Plan at NA-MIC project week](https://projectweek.na-mic.org/PW34_2020_Virtual/Projects/SlicerLiverAnalysis/) (December 2020)
1. Palomar, Rafael, et al. "A novel method for planning liver resections using deformable Bézier surfaces and distance maps." Computer Methods and Programs in Biomedicine 144 (2017): 135-45.
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2 changes: 1 addition & 1 deletion PW37_2022_Virtual/Projects/SlicerTMS/README.md
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Expand Up @@ -44,7 +44,7 @@ Real-time visualization of an electric field (E-field) for transcranial magnetic

#### Coil moving and updating the electric field on the brain surface inside slicer:

<img src="./tms_vis.gif" width="500" alt="Brain surface coil moving">
<img src="https://github.com/NA-MIC/ProjectWeek/releases/download/project-week-resources/PW37__SlicerTMS__tms_vis.gif" width="500" alt="Brain surface coil moving">


#### Started WebSocket Tests: we can interact with the red, green and yellow slices with the new websocket connection:
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6 changes: 5 additions & 1 deletion PW37_2022_Virtual/Projects/StreamlinedROIAnnotationTool/README.md
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Expand Up @@ -55,6 +55,7 @@ as possible.
and image information back to server.

## Next Steps

1. Need to add scoring functionality (DONE)
2. Need to add way to mark image as defective (DONE)
3. Need to add way to clear Previously added ROIs (DONE w/help from erikz)
Expand All @@ -65,15 +66,18 @@ as possible.


# Illustrations

<p align="center">
<img src="work_flow.png" />
</p>

Demo video from start of project:
![](SimplifiedROITool.gif)
![](roi-web-tool-example.gif)

Demo video from end of project:
![](FinalROITool_1.gif)
![](https://github.com/NA-MIC/ProjectWeek/releases/download/project-week-resources/PW37__StreamlinedROIAnnotationTool__FinalROITool_1.gif)

# Background and References

<!-- If you developed any software, include link to the source code repository. If possible, also add links to sample data, and to any relevant publications. -->
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Expand Up @@ -18,7 +18,7 @@ https://drive.google.com/file/d/1A7-8Ru0uTJHFFa17rZtkBpvNhJao_F7x/view?usp=share
Creating a cohort or tagging DICOM images is a very time-consuming and error-prone procedure.
In this project, we are extending the functionality of the so-called Gallery View within Kaapana.

![](NA-MIC.gif)
![](https://github.com/NA-MIC/ProjectWeek/releases/download/project-week-resources/PW38__KaapanaFastViewingAndTaggingOfDICOMImages__NA-MIC.gif)

## Approach and Plan

Expand Down Expand Up @@ -55,4 +55,4 @@ tbd

# Background and References

https://github.com/kaapana/kaapana
https://github.com/kaapana/kaapana
2 changes: 2 additions & 0 deletions PW38_2023_GranCanaria/Projects/MONAILabel2bundle/README.md
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Expand Up @@ -67,12 +67,14 @@ Figure 1 - Full CT segmentation on subject from spleen decathalon data

Figure 2 - Comparison on spleen decathalon data of the MONAI full CT segmentation bundle we created (left) to the output TotalSegmentator produces (right)
[monai_bundle_vs_total_seg_spleen.webm](https://user-images.githubusercontent.com/59979551/216606510-047a0105-17ca-4765-8186-4132edf2c0e9.webm)
![](https://github.com/NA-MIC/ProjectWeek/releases/download/project-week-resources/PW38__MONAILabel2bundle__monai_bundle_vs_total_seg_spleen.gif)

Figure 3 - Full CT segmentation on subject from IDC
![02_03_23_full_ct_segmentation_success_idc](https://user-images.githubusercontent.com/59979551/216612414-649813e5-945b-4719-aaa8-8954aeb44d18.JPG)

Figure 4 - Comparison on IDC data of the MONAI full CT segmentation bundle we created (left) to the output TotalSegmentator produces (right)
[monai_bundle_vs_total_seg_idc.webm](https://user-images.githubusercontent.com/59979551/216612449-013d7dad-7bc6-43b0-9780-0c9f9b848007.webm)
![](https://github.com/NA-MIC/ProjectWeek/releases/download/project-week-resources/PW38__MONAILabel2bundle__monai_bundle_vs_total_seg_idc.gif)

## Discussion notes

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