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Update README.md
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fedorov authored Jun 28, 2024
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Expand Up @@ -91,7 +91,7 @@ IDC provides a growing amount of publicly available cancer imaging data (>65TB a
1. Update [MHub+IDC tutorial](https://github.com/MHubAI/examples/blob/main/notebooks/PW41_tutorial.ipynb) in how it accesses IDC.
1. Prepared initial version of the query to extract processing steps for slide microscopy (SM) images using DICOM metadata ([https://github.com/ImagingDataCommons/idc-index-data/pull/30](https://github.com/ImagingDataCommons/idc-index-data/pull/30)). When completed, this will allow selecting SM images by embedding method, staining (H&E), and fixative without using BigQuery, and with queries of significantly lower complexity as compared to querying full index.
2. Implemented new feature in the dcmqi converter that allows including into DICOM SEG references to the segmented images when geometry of the segmentation is different from the image (e.g., when segmentation was done on the slices orthogonal to the segmented image) ([https://github.com/QIICR/dcmqi/issues/489](https://github.com/QIICR/dcmqi/issues/489)). Lacking this feature, ReMIND collection encoded images that are disconnected from the segmented MR images.
3. Mapped model-specific segmentation labels for [OMAS](https://docs.google.com/spreadsheets/d/1pBicNskjMDJBnD3w4yAQroj8SGSAhDfA_TUK24dLEyc/edit?gid=1390863317#gid=1390863317) and [TotalSegmentator](https://docs.google.com/spreadsheets/d/1oEzXCmraoLgbbb5lNxWiHuYDza86aXxKqSUmUetwI7M/edit?gid=780795691#gid=780795691) to SNOMED-CT (related PRs [https://github.com/wasserth/TotalSegmentator/pull/324](https://github.com/wasserth/TotalSegmentator/pull/324) and [https://github.com/wasserth/TotalSegmentator/pull/325](https://github.com/wasserth/TotalSegmentator/pull/325)).
3. Mapped model-specific segmentation labels for [OMAS](https://docs.google.com/spreadsheets/d/1pBicNskjMDJBnD3w4yAQroj8SGSAhDfA_TUK24dLEyc/edit?gid=1390863317#gid=1390863317) and [TotalSegmentator](https://docs.google.com/spreadsheets/d/1oEzXCmraoLgbbb5lNxWiHuYDza86aXxKqSUmUetwI7M/edit?gid=780795691#gid=780795691) to SNOMED-CT (related PRs [https://github.com/wasserth/TotalSegmentator/pull/324](https://github.com/wasserth/TotalSegmentator/pull/324) and [https://github.com/wasserth/TotalSegmentator/pull/325](https://github.com/wasserth/TotalSegmentator/pull/325)). Those interested to map labels from their model can follow instructions in [https://qiicr.gitbook.io/dcmqi-guide/opening/coding_schemes/searching_codes_outside_dicom](https://qiicr.gitbook.io/dcmqi-guide/opening/coding_schemes/searching_codes_outside_dicom) and of course contact Andrey and/or ask questions on the [IDC forum](https://discourse.canceridc.dev/).
4. Presented IDC updates at the Thu breakout session (see notes and references in [this document](https://docs.google.com/document/d/11IG53uKYePUlQFCUX6nFw4HqQDyt2jcLkvqjnHGNPCI/edit)).
5. Reviewed beta (aka pita) release of the [pydcmqi](https://github.com/LennyN95/pydcmqi) python wrapper of dcmqi prepared by Leo. pydcmqi aims to simplify pythonic access to dcmqi functionality.

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