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SAM3 semantic segmentation tool#221

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yvanlebras merged 46 commits intogalaxyecology:masterfrom
TuturBaba:Sam3
Mar 5, 2026
Merged

SAM3 semantic segmentation tool#221
yvanlebras merged 46 commits intogalaxyecology:masterfrom
TuturBaba:Sam3

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@TuturBaba
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This pull request adds a new Galaxy tool called SAM3 Semantic Segmentation.
The tool performs text-prompted semantic segmentation on images or videos using the SAM3 model.

Users can provide one or more images or a single video, along with a text prompt describing the object to segment.
The tool supports multiple output formats, including COCO annotations and YOLO bounding boxes or segmentation masks.

Comment thread tools/Sam3/sam3_video_semantic_segmentation.xml Outdated
Comment thread tools/Sam3/sam3_video_semantic_segmentation.xml Outdated
Comment thread tools/Sam3/sam3_video_semantic_segmentation.xml Outdated
Comment thread tools/Sam3/sam3_video_semantic_segmentation.xml Outdated
Comment thread tools/Sam3/sam3_video_semantic_segmentation.xml Outdated
Comment thread tools/Sam3/sam3_video_semantic_segmentation.xml Outdated
Comment thread tools/Sam3/sam3_video_semantic_segmentation.xml Outdated
Comment thread tools/Sam3/sam3_video_semantic_segmentation.xml Outdated
@TuturBaba TuturBaba marked this pull request as draft February 11, 2026 09:46
@TuturBaba TuturBaba assigned TuturBaba and unassigned TuturBaba Feb 19, 2026
@TuturBaba TuturBaba marked this pull request as ready for review February 19, 2026 10:02
@TuturBaba
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Hello @bgruening , the pull request looks good overall. The only thing I'm not sure about is the handling of the SAM3 model.

Comment thread tools/Sam3/sam3_semantic_segmentation.py
Comment thread tools/Sam3/sam3_semantic_segmentation.xml Outdated
@bgruening
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What do you mean with the SAM model? The admins need to install them manually into the correct path and modify the location file accordingly.

@TuturBaba
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What do you mean with the SAM model? The admins need to install them manually into the correct path and modify the location file accordingly.

Does it have to be available on Hugging Face, or is it just a preferred practice?

@bgruening
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Best practice I would say, the model can be elsewhere. We just need to communicate this to the Admin that has to configure it.

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@yvanlebras

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THANK YOU Arthur! Seems to me ok. Just 2 comments to add fundings (as it seems to me we can now do that in tool xml) + looking at space after commas on example prompt (and maybe related python script to see if there is no issues managing space removing or others)

Comment thread tools/Sam3/sam3_semantic_segmentation.xml
Comment thread tools/Sam3/sam3_semantic_segmentation.xml
Comment thread tools/Sam3/sam3_semantic_segmentation.xml Outdated
Comment thread tools/Sam3/sam3_semantic_segmentation.xml Outdated
@yvanlebras
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THANK YOU Arthur, Björn, Pauline ! This seems to me ok for a first version of tool in production in Galaxy Ecology!

@yvanlebras yvanlebras merged commit 2c1362b into galaxyecology:master Mar 5, 2026
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4 participants