# LungCTAnalyzer extension for lung CT segmentation and analysis for COVID-19 assessment
**URL:** https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006
**Category:** Support
**Tags:** feature, lungctanalyzer
**Created:** [December 11, 2020, 5:33pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006 "2020-12-11T17:33:10Z")
**Posts on this page:** 20
**Page:** 1
### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [December 11, 2020, 5:33pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/1 "2020-12-11T17:33:10Z")
New extension is added for lung CT segmentation and analysis for COVID-19 assessment. It is developed by Prof. Rudolf Bumm (@rbumm), a clinician in KSGR (Chur, Switzerland; with some help from Slicer core developers to polish things up), which is a nice demonstration of how Python scripting in Slicer allows users to quickly develop clinically deployable tools from their ideas.
The extension offers a quick (1-minute) lung segmentation wizard and quantitative volumetric analysis of the lungs with quick slice and volume rendering visualization and PDF report generation.
Extension webpage: [GitHub - rbumm/SlicerLungCTAnalyzer: This is a 3D Slicer extension for segmentation and spatial reconstruction of infiltrated, collapsed, and emphysematous areas in lung CT.](https://github.com/rbumm/SlicerLungCTAnalyzer)
Demo video:
[ ](https://www.youtube.com/watch?v=fpLxm7uAvZQ)
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### Author:  [@TMrt](https://discourse.slicer.org/u/TMrt)
#### Post date: [December 11, 2020, 7:03pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/2 "2020-12-11T19:03:20Z")
I just tried this out-amazing! Thank you
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### Author:  [@rbumm](https://discourse.slicer.org/u/rbumm)
#### Post date: [December 12, 2020, 5:03pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/3 "2020-12-12T17:03:02Z")
Thanks for the mention, @lassoan, and thanks for the great cooperation. I pushed several small improvements to Github.
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### Author:  [@Khaldoun](https://discourse.slicer.org/u/Khaldoun)
#### Post date: [December 13, 2020, 6:15pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/4 "2020-12-13T18:15:13Z")
Hi, I am very new and naive to 3D slicer. I just installed the last stable version on Mac OS
and installed the Chest Imaging Platform but i could not find the Lung CT analyser extension for lung CT segmentation and analysis. I checked the extension webpage on GitHub but I don’t know how to install the extensions in 3D Slicer from the files after dowonloading the zip files. By the way I also hardly see the modules in Module finder as they look as ghost icons. Is it a matter of OS ? I am using a Mac Book Pro with 16 Go ram under Mac OS High sierra 10.13.6
Sorry for being at a starter point and thank you for your help
The demo video looks amazing and I am impatient to try it
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### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [December 13, 2020, 6:36pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/5 "2020-12-13T18:36:04Z")
> [@Khaldoun](#):
>
> i could not find the Lung CT analyser extension for lung CT segmentation and analysis
Lung CT analyzer is available for latest Slicer Preview Release (extension name: LungCTAnalyzer, in Chest Imaging Platform category).
> [@Khaldoun](#):
>
> By the way I also hardly see the modules in Module finder as they look as ghost icons. Is it a matter of OS ? I
This is a [known issue](https://github.com/Slicer/Slicer/issues/5118), a workaround is to change your system to dark mode.
@rbumm This extension may bring in users that are new to Slicer and therefore it would be useful if you could add a few sentences about how to install the extension to the [extension documentation page](https://github.com/rbumm/SlicerLungCTAnalyzer/edit/master/README.md). Until now, the extension was only submitted to the Slicer-4.13 extensions index, but I’ve added it not to the Slicer-4.11 extensions index now, so from tomorrow it should show up for the latest stable Slicer version (Slicer-4.11.20200930).
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### Author:  [@Khaldoun](https://discourse.slicer.org/u/Khaldoun)
#### Post date: [December 13, 2020, 8:12pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/6 "2020-12-13T20:12:39Z")
Hi Andras
Thank you very much for you so quick reply
Very clear !
I am a nuclear medicine physician and my aim is to use 3D slicer and CIP for lobar quantification of Lung ventilation/perfusion scans by combining lobar lung segmentation and quantification extensions. If you have suggestions I’ll be glad to follow them
Congratulations for the great job you did and are doing with 3D slicer
Khaldoun
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### Author:  [@rbumm](https://discourse.slicer.org/u/rbumm)
#### Post date: [December 13, 2020, 8:42pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/7 "2020-12-13T20:42:56Z")
@lassoan I added a description on the extension documentation page. I will add a few screenshots later. Hope I did it right, would we have to comment on [https://slicer.kitware.com/midas3/slicerappstore](https://slicer.kitware.com/midas3/slicerappstore) too ?
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### Author:  [@rbumm](https://discourse.slicer.org/u/rbumm)
#### Post date: [December 13, 2020, 8:46pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/8 "2020-12-13T20:46:35Z")
Oh @lassoan I just see that you added it to the extension index, so it will appear “normally” if you “Install slicer extensions” from 3D slicer “Welcome” page ?
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### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [December 13, 2020, 8:47pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/9 "2020-12-13T20:47:38Z")
Yes, the extension is already available in the extension manager for 4.13 and will be available for 4.11 from tomorrow. So, there is no need to describe the manual installation steps, only installation via the Extensions Manager in Slicer. Thank you!
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### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [December 14, 2020, 2:06am UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/10 "2020-12-14T02:06:08Z")
> [@Khaldoun](#):
>
> I am a nuclear medicine physician and my aim is to use 3D slicer and CIP for lobar quantification of Lung ventilation/perfusion scans by combining lobar lung segmentation and quantification extensions. If you have suggestions I’ll be glad to follow them
Thanks for the introduction. Slicer and its extension should be able to help you with these. Post separate topics with specific questions if you need help.
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### Author:  [@Javi\_Vicente](https://discourse.slicer.org/u/Javi_Vicente)
#### Post date: [January 11, 2021, 1:02pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/11 "2021-01-11T13:02:47Z")
What parameters should I look at to know if the patient has covid?
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### Author:  [@rbumm](https://discourse.slicer.org/u/rbumm)
#### Post date: [January 11, 2021, 1:49pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/12 "2021-01-11T13:49:40Z")
After running the Lung CT Analyzer, there is an option (button) to display the “COVID-19 Results Table”. In Slicer’s COVID-19 demo dataset you would get:
| Results | right (ml) | right (%) | left (ml) | left (%) | total (ml) | total (%) |
| --- | --- | --- | --- | --- | --- | --- |
| Lung volume | 3857 | 51 | 3675 | 49 | 7532 | 100 |
| Functional volume | 2104 | 55 | 2874 | 78 | 4978 | 66 |
| Affected volume | 1846 | 48 | 854 | 23 | 2700 | 36 |
| CovidQ (affected / functional) | 0.88 | -1 | 0.3 | -1 | 0.54 | -1 |
COVID-Q is higher in the right lung compared to the left lung. This corresponds well with the extent of infiltrations on the right side.
Please understand that this computation is for scientific use only, it has been implemented only recently and needs validation in clinical studies.
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### Author:  [@yangyang117](https://discourse.slicer.org/u/yangyang117)
#### Post date: [May 25, 2021, 6:09am UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/13 "2021-05-25T06:09:45Z")
hi, It is great work. I think the CT is segmented by threshold or other traditional tech,right? I found its still have some cavity in the segmentation.Is there any way to segment the lobes and PA,Aorta?
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### Author:  [@rbumm](https://discourse.slicer.org/u/rbumm)
#### Post date: [May 25, 2021, 8:47am UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/14 "2021-05-25T08:47:53Z")
Hi,
The “Lung CT Segmenter” currently produces lung masks only by a grow from seeds function. The masks are used in “Lung CT Analyzer” for creating thresholded segments of lung parenchyma.
If the lung masks have dents, missing parts or leaks you can place additional fiducials (right lung, left lung, other = outside) before you press “Apply” to correct this. You can also change the lung intensity range slider to prevent leaks.
If you need to segment lung lobes you may try “Interactive Lobe Segmentation” from the “Chest Imaging Platform”. This is from different developers and also works quite well.
Best regards
Rudolf
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### Author:  [@rbumm](https://discourse.slicer.org/u/rbumm)
#### Post date: [May 25, 2021, 8:53am UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/15 "2021-05-25T08:53:28Z")
For PA, Aorta, PV you would need a very good contrast CT and could segment the vessels by producing a vessel mask and then use “Grow from Seeds” like shown in this video:
[ ](https://www.youtube.com/watch?v=wS6-4dwZCfo)
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### Author:  [@franx](https://discourse.slicer.org/u/franx)
#### Post date: [May 25, 2021, 6:41pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/16 "2021-05-25T18:41:26Z")
Hi, I was trying to use this extension in order to predict covid, but the “COVID results table” button doesn’t appears in my slicer extension installation. Instead of this appears a button for “extended result table” ([Screenshot - d0be934391961b2497048209faef2979 - Gyazo](https://gyazo.com/d0be934391961b2497048209faef2979)). It is an error? Or it has been removed?
Thanks.
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### Author:  [@rbumm](https://discourse.slicer.org/u/rbumm)
#### Post date: [May 25, 2021, 9:36pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/17 "2021-05-25T21:36:13Z")
Hi Fran,
the COVID results table was renamed because it could also be used in conditions like Pneumonia, measuring infiltrations or ARDS, and be useful in COPD. The data in the table have not changed much and can be used in COVID.19 disease. Systematic evaluations are under way. A high relative affection rate (infiltrated + collapsed, \> 50 %) in % of total lung tissue indicates advanced cases. High collapse rates (10-20%) are often seen in fatal cases.
Best regards
rudolf
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### Author:  [@franx](https://discourse.slicer.org/u/franx)
#### Post date: [May 25, 2021, 9:46pm UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/18 "2021-05-25T21:46:23Z")
Ok, I get that it is better to look at the percentage of several injuries than in a single parameter of the covid. Thanks for the answer, the work is great!
Fran
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### Author:  [@mahmoud](https://discourse.slicer.org/u/mahmoud)
#### Post date: [September 6, 2021, 12:08am UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/19 "2021-09-06T00:08:00Z")
> [@rbumm](#):
>
> Systematic evaluations are under way. A high relative affection rate (infiltrated + collapsed, \> 50 %) in % of total lung tissue indicates advanced cases. High collapse rates (10-20%) are often seen in fatal cases.
thans prof rbumm
please can you give your email to important disscution in this extention
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### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [September 6, 2021, 12:45am UTC](https://discourse.slicer.org/t/lungctanalyzer-extension-for-lung-ct-segmentation-and-analysis-for-covid-19-assessment/15006/20 "2021-09-06T00:45:09Z")
> [@mahmoud](#):
>
> please can you give your email
Please keep the discussion open, to allow others to learn from and contribute to the discussion. Switch to private messages only if you need to talk about personal or confidential matters.
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