Holoscan Sample App Data for AI-based Endoscopy Tool Tracking

This resource contains the convolutional LSTM model for tool tracking in laparoscopic videos by Nwoye et. al [1], and a sample surgical video.

\n
[1] Nwoye, C.I., Mutter, D., Marescaux, J. and Padoy, N., 2019. Weakly supervised convolutional LSTM approach for tool tracking in laparoscopic videos. International journal of computer assisted radiology and surgery, 14(6), pp.1059-1067
\n

Model

The AI model for instrument tracking in endoscopy is an LSTM model which given an RGB image of 854 x 480 provides

per-instrument detection probability,
per-instrument detected tooltip location,
semantic segmentation of the instruments.\nEach pixel stores 7 labels.

Note: The provided model is in ONNX format. It will automatically be converted into a TensorRT model (.engine) the first time it is processed by a Holoscan application.

Inputs

data_ph:0 - Input RGB image ( batchsize, height, width, channels)\n
- shape=[1, 480, 854, 3]
- dtype=float32
- range=[0, 255]
\n
cellstate_ph:0 - LSTM hidden state tensor 0\n
- shape=[1, 60, 107, 7]
- dtype=float32
\n
hiddenstate_ph:0 - LSTM hidden state tensor 1\n
- shape=[1, 60, 107, 7]
- dtype=float32
\n

Outputs

Model/net_states:0 - LSTM output state tensor. Output of frame N is input for frame N + 1.\n
- shape=[1, 60, 107, 7]
- dtype=float32
\n
Model/net_states:0 - LSTM hidden state tensor. Output of frame N is input for frame N + 1.\n
- shape=[1, 60, 107, 7]
- dtype=float32
\n
probs:0 - Per instrument detection probability\n
- shape=[1, 7]
- dtype=float32
- range=[0,1]
\n
Localize/scaled_coords:0 - Per-instrument (x,y) detected tooltip location\n
- shape=[1, 2, 7]
- dtype=float32
\n
Localize_1/binary_masks:0 - image with per instrument segmentation mask. Each pixel stores 7 labels\n
- shape=[1, 60, 107, 7]
- dtype=float32
\n

Video Data

The sample data, kindly provided by Research Group Camma, IHU Strasbourg and University of Strasbourg, is a surgical video that includes all 7 instruments classes supported by the tool tracking model. It's in a raw H264 format.

Note: the .h264 file must be converted into a GXF tensor file using the convert_video_to_gxf_entities.py script on GitHub to be used with the VideoStreamReplayer Holoscan operator.

License

Refer to the license agreement for use of the sample data.

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Weakly supervised convolutional LSTM approach for tool tracking in laparoscopic videos. International journal of computer assisted radiology and surgery, 14(6), pp.1059-1067](https://link.springer.com/article/10.1007/s11548-019-01958-6)\n\n## Model\n\nThe AI model for instrument tracking in endoscopy is an LSTM model which given an RGB image of `854 x 480` provides\n- per-instrument detection probability,\n- per-instrument detected tooltip location,\n- semantic segmentation of the instruments.\nEach pixel stores 7 labels.\n\n_Note: The provided model is in ONNX format. It will automatically be converted into a TensorRT model (.engine) the first time it is processed by a Holoscan application._\n\n### Inputs\n\n- `data_ph:0` - Input RGB image ( batchsize, height, width, channels)\n - `shape=[1, 480, 854, 3]`\n - `dtype=float32`\n - `range=[0, 255]`\n- `cellstate_ph:0` - LSTM hidden state tensor 0\n - `shape=[1, 60, 107, 7]`\n - `dtype=float32`\n- `hiddenstate_ph:0` - LSTM hidden state tensor 1\n - `shape=[1, 60, 107, 7]`\n - `dtype=float32`\n\n### Outputs\n\n- `Model/net_states:0` - LSTM output state tensor. Output of frame `N` is input for frame `N + 1`.\n - `shape=[1, 60, 107, 7]`\n - `dtype=float32`\n- `Model/net_states:0` - LSTM hidden state tensor. Output of frame `N` is input for frame `N + 1`.\n - `shape=[1, 60, 107, 7]`\n - `dtype=float32`\n- `probs:0` - Per instrument detection probability\n - `shape=[1, 7]`\n - `dtype=float32`\n - `range=[0,1]`\n- `Localize/scaled_coords:0` - Per-instrument (x,y) detected tooltip location\n - `shape=[1, 2, 7]`\n - `dtype=float32`\n- `Localize_1/binary_masks:0` - image with per instrument segmentation mask. Each pixel stores 7 labels\n - `shape=[1, 60, 107, 7]`\n - `dtype=float32`\n\n## Video Data\n\nThe sample data, kindly provided by [Research Group Camma](http://camma.u-strasbg.fr), [IHU Strasbourg](https://www.ihu-strasbourg.eu/) and [University of Strasbourg](https://en.unistra.fr/), is a surgical video that includes all 7 instruments classes supported by the tool tracking model. It's in a raw H264 format.\n\n_Note: the .h264 file must be converted into a GXF tensor file using the `convert_video_to_gxf_entities.py` script on [GitHub](https://github.com/nvidia-holoscan/holoscan-sdk/tree/main/scripts#convert_video_to_gxf_entitiespy) to be used with the `VideoStreamReplayer` Holoscan operator._\n\n## License\n\nRefer to the [license agreement](https://developer.nvidia.com/clara-holoscan-EULA) for use of the sample data.","displayName","Endoscopy Sample App Data",["D",1681919746426],"publisher","NVIDIA","latestVersion","versions","collectionCounts","imageUrl","/api/image/nvidia/clara-holoscan/resources/holoscan_endoscopy_sample_data","rawImageUrl","https://avatars.githubusercontent.com/u/119712212","canGuestDownload","latestVersionSizeInBytes","licenseTerms","isMultinodeEnabled","isMultiArchitecture","bias","explainability","privacy","safetyAndSecurity","featureLabels",[],"displayLabels",[266,267,268,269,270],"policyLabels",[],"systemLabels",[],"products",[],"hasNimMetadata",{"_234":291,"_272":292,"_274":293,"_276":277},{"_234":288,"_272":289,"_274":290,"_276":277},{"_234":284,"_272":285,"_274":286,"_276":277},{"_234":280,"_272":281,"_274":282,"_276":277},{"_234":271,"_272":273,"_274":275,"_276":277},"Holoscan","value","pltfm_clara_holoscan","filter",{"_278":279,"_272":273},"category","label","field","platform","Healthcare","indus_healthcare",{"_278":283,"_272":281},"industry","DL","soln_dl",{"_278":287,"_272":285},"technology","Clara","pltfm_clara",{"_278":279,"_272":289},"AI","soln_ai",{"_278":287,"_272":292},{"_126":1467,"_128":1468},"ngcApps",[1420],"csaApiBaseUrl","https://www.nvidia.com/ai-agents/csa-agent/dcsm","datadogRum",{"_1401":1402,"_1403":1404,"_1405":1406,"_1407":1408,"_1409":305,"_157":329,"_1410":1411,"_1412":57,"_1413":105,"_1414":105,"_1415":1416,"_1417":105,"_1418":1419},"amplitude",{"_1398":1399,"_1000":-7,"_1400":32},"disableJs","environment","prod","featureFlagsBlob","JTdCJTIydGVzdEZsYWclMjIlM0FmYWxzZSUyQyUyMnNob3dTZWFyY2hMYWJlbFNldEZpbHRlcnMlMjIlM0FmYWxzZSUyQyUyMmNoaW5hTmltRGlzdHJpYnV0b3JzUmVkZXNpZ24lMjIlM0F0cnVlJTJDJTIyZW5hYmxlQ3NhV2lkZ2V0JTIyJTNBZmFsc2UlMkMlMjJlbmFibGVQcm9kdWN0R3JvdXBpbmdCeVN1YnNjcmlwdGlvbiUyMiUzQWZhbHNlJTJDJTIyY29udGFpbmVyU2Nhbm5pbmdSZWRlc2lnbk0xJTIyJTNBdHJ1ZSU3RA==","featureFlagsGuarded","isDevLikeEnv","isPlaywright","isMobileDevice","categorizedOrgs",{"_1392":1393,"_1394":1395,"_1396":1397},"currentOrgContext","currentContextRoles",[],"enterpriseOrgs",[],"locale","en","ngcApiOrigin","ngcHelmOrigin","origin","https://catalog.ngc.nvidia.com","usesMocks","theme","year",2026,"1.7.3","defaultSearchSuggestions",{"_1275":201,"_1276":1277,"_1278":1279,"_1280":1281},"announcements",[],"consentState",{"_366":1265,"_1266":105,"_1267":32,"_1268":32,"_1269":1270},"consentConfig",{"_348":349,"_350":351,"_352":353,"_354":355,"_356":357,"_358":359,"_360":361,"_362":363,"_364":365,"_366":367},"showContactAdmin",1783955692698,[],[],[343,344,345,346,347],{"_46":60,"_48":71,"_50":121,"_52":-5,"_54":-5,"_56":57},{"_46":60,"_48":69,"_50":121,"_52":-5,"_54":-5,"_56":57},{"_46":60,"_48":61,"_50":121,"_52":-5,"_54":-5,"_56":57},{"_46":58,"_48":59,"_50":121,"_52":-5,"_54":-5,"_56":57},{"_46":47,"_48":49,"_50":121,"_52":-5,"_54":-5,"_56":57},"mainInfoText","We and our third-party partners (including social media, advertising, and analytics partners) use cookies and other tracking technologies to collect, store, monitor, and process certain information about you when you visit our website. 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Name	Size	Updated	Actions
CAMMA_LSTM_Model.png	25.75 KB	March 17, 2023 UTC	curl wget Download
NVIDIA-Clara-Holoscan-SDK-EULA.pdf	155.83 KB	March 17, 2023 UTC	curl wget Download
surgical_video.264	4.42 MB	March 17, 2023 UTC	curl wget Download
tool_loc_convlstm.onnx	42.68 MB	March 17, 2023 UTC	curl wget Download