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# `pixels` Solution Accelerator
✅ Ingest and index DICOM image metadata (.dcm and from zip archives)
</br> ✅ Analyze DICOM image metadata with SQL and Machine Learing.
</br> ✅ Analyze DICOM image metadata with SQL and Machine Learning.
</br> ✅ View, segment, label DICOM Images with OHIF viewer integrated into Lakehouse Apps and Databricks security model.
</br> ✅ One button push to lauch model training from OHIF viewer.
</br> ✅ One button push to launch model training from OHIF viewer.
</br> ✅ NVIDIA's [MONAI](https://docs.nvidia.com/monai/index.html) Integration, AI to automatically segment medical images and train custom models.
</br> ✅ Leverage Databricks' [Model Serving](https://docs.databricks.com/en/machine-learning/model-serving/index.html), hosting NVIDIA's MONAI in serverless GPU enabled clusters for real-time segmentation.
</br> ✅ Leverage Databricks' [Model Serving](https://docs.databricks.com/en/machine-learning/model-serving/index.html) with serverless GPU enabled clusters for real-time segmentation.

---
## Secure Lakehouse integrated DICOM Viewer powered by OHIF
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To start the OHIF Viewer web app you need to:
- Execute the [06-OHIF-Viewer](https://github.com/databricks-industry-solutions/pixels/blob/main/06-OHIF-Viewer.py) inside a Databricks workspace.
- Set `table` parameter with full name of you pixels catalog table. Ex: `main.pixels_solacc.object_catalog`
- Set `sqlWarehouseID`parameter to execute the queries required to collect the records. It's the final section of the `HTTP path` in the `Connection details` tab. Use [Serverless](https://docs.databricks.com/en/admin/sql/warehouse-types.html#sql-warehouse-types) for best performance.
- Set the `table` parameter to the full name of your Pixels catalog table. Ex: `main.pixels_solacc.object_catalog`
- Set the `sqlWarehouseID`parameter to execute the queries required to collect the records. It's the final section of the `HTTP path` in the `Connection details` tab. Use [Serverless](https://docs.databricks.com/en/admin/sql/warehouse-types.html#sql-warehouse-types) for best performance.

<img src="https://github.com/databricks-industry-solutions/pixels/blob/main/images/sqlWarehouseID.png?raw=true" alt="sqlWarehouseID"/>

- Use the link generated in the last notebook to access the OHIF viewer page.

## Save measurements and segmentations
The OHIF Viewer allows you to save back in databricks the measurements and the segmentations created in the viewer.
The OHIF Viewer allows you to save back to Databricks the measurements and the segmentations created in the viewer.
The metadata will be stored in the object_catalog, and the generated dicom files in the volume under the path `/ohif/exports/`.

<img src="https://github.com/databricks-industry-solutions/pixels/blob/main/images/ohif_save_segm.png?raw=true" alt="OHIF_SAVE_SEG" height="300"/>
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- Customizable Workflows: Tailor the annotation process to fit specific research needs.

### MONAILabel Setup Instructions
To execute the MONAILabel server is mandatory to use a cluster with Databricks Runtime Version of `14.3 LTS ML`. For the best performance use a [GPU-Enabled compute](https://docs.databricks.com/en/compute/gpu.html#gpu-enabled-compute).
To execute the MONAILabel server it is mandatory to use a cluster with Databricks Runtime Version of `14.3 LTS ML`. For the best performance use a [GPU-Enabled compute](https://docs.databricks.com/en/compute/gpu.html#gpu-enabled-compute).
#### Start the MONAILabel server
- Execute the [05-MONAILabel](https://github.com/databricks-industry-solutions/pixels/blob/main/05-MONAILabel.py) inside a Databricks workspace.
- Set `table` parameter with full name of you pixels catalog table. Ex: `main.pixels_solacc.object_catalog`
- Set `sqlWarehouseID`parameter to execute the queries required to collect the records. Use [Serverless](https://docs.databricks.com/en/admin/sql/warehouse-types.html#sql-warehouse-types) for best performance.
- Set the `table` parameter to the full name of your Pixels catalog table. Ex: `main.pixels_solacc.object_catalog`
- Set the `sqlWarehouseID`parameter to the DBSQL Warehouse ID, needed to run queries required to collect the records. Use [Serverless](https://docs.databricks.com/en/admin/sql/warehouse-types.html#sql-warehouse-types) for best performance.
<img src="https://github.com/databricks-industry-solutions/pixels/blob/main/images/sqlWarehouseID.png?raw=true" alt="sqlWarehouseID">
#### Open the OHIF Viewer
- Execute the notebook [06-OHIF-Viewer](https://github.com/databricks-industry-solutions/pixels/blob/main/06-OHIF-Viewer.py) to start the OHIF Viewer with the MONAILabel extension and open the generated link.
- Select the preferred CT scan study and press on `MONAI Label` button.
- Select the preferred CT scan study and press the `MONAI Label` button.

<img src="https://github.com/databricks-industry-solutions/pixels/blob/main/images/monailabel_btn.png?raw=true" alt="MONAI_BTN" height="250"/></br>
#### Connect, execute and save
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| library | purpose | license | source |
|----------------------|-------------------------------------|-------------------------------|---------------------------------------------------------|
| dbx.pixels | Scale out image processong Spark | Databricks | https://github.com/databricks-industry-solutions/pixels |
| dbx.pixels | Scale out image processing library | Databricks | https://github.com/databricks-industry-solutions/pixels |
| pydicom | Python api for DICOM files | MIT | https://github.com/pydicom/pydicom |
| python-gdcm | Install gdcm C++ libraries | Apache Software License (BSD) | https://github.com/tfmoraes/python-gdcm |
| gdcm | Parse DICOM files | BSD | https://sourceforge.net/projects/gdcm |
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