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1 | 1 | # Pathology Use Case
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2 | 2 |
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3 |
| -> _This App is currently under active development._ |
4 |
| -
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5 | 3 | ### Overview
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6 | 4 |
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7 | 5 | This is a reference app to run infer + train tasks to segment Nuclei. It comes with following 2 pre-trained
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@@ -47,20 +45,21 @@ cd MONAILabel
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47 | 45 | pip install -r requirements.txt
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48 | 46 | ```
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49 | 47 |
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50 |
| -> Install [Openslide](https://openslide.org/) binaries manually and make sure .dll or .so files for openslide are in system load path. For windows, make sure **<openslide_folder>**/bin is added in PATH environment. |
51 |
| -> For ubuntu: `apt install openslide-tools` |
| 48 | +> Install [Openslide](https://openslide.org/) binaries manually and make sure .dll or .so files for openslide are in system load path. |
| 49 | +> - For windows, make sure **<openslide_folder>**/bin is added in PATH environment. |
| 50 | +> - For ubuntu: `apt install openslide-tools` |
52 | 51 |
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53 | 52 | #### FileSystem as Datastore
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54 | 53 |
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55 | 54 | ```bash
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56 |
| - # download sample wsi image (skip this if you already have some) |
57 |
| - mkdir sample_wsi |
58 |
| - cd sample_wsi |
59 |
| - wget https://demo.kitware.com/histomicstk/api/v1/item/5d5c07539114c049342b66fb/download |
60 |
| - cd - |
61 |
| - |
62 |
| - # run server |
63 |
| - ./monailabel/scripts/monailabel start_server --app sample-apps/pathology --studies datasets/wsi |
| 55 | +# download sample wsi image (skip this if you already have some) |
| 56 | +mkdir sample_wsi |
| 57 | +cd sample_wsi |
| 58 | +wget https://demo.kitware.com/histomicstk/api/v1/item/5d5c07539114c049342b66fb/download |
| 59 | +cd - |
| 60 | + |
| 61 | +# run server |
| 62 | +./monailabel/scripts/monailabel start_server --app sample-apps/pathology --studies datasets/wsi |
64 | 63 | ```
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65 | 64 |
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66 | 65 | ###### QuPath
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@@ -123,3 +122,23 @@ Analysis Page.
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123 | 122 |
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124 | 123 | 
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125 | 124 |
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| 125 | + |
| 126 | +### Performance Benchmarking |
| 127 | + |
| 128 | +The performance benchmarking is done using MONAILabel server and DSA client. All the details are |
| 129 | +captured [here](https://docs.google.com/spreadsheets/d/1TeSOGzcTeeIThEvd_eflJNx0hhZiELNGBiYzwKyYEFg/edit?usp=sharing). |
| 130 | + |
| 131 | +Following is summary of the same: |
| 132 | + |
| 133 | +- NucleiDetection (CPU Based DSA Algorithm) |
| 134 | +- Segmentation/DeepEdit (MONAILabel models) |
| 135 | + |
| 136 | +<table> |
| 137 | +<tr> |
| 138 | +<td colspan="2"><img src="../../docs/images/DSAPerf1.png"/></td> |
| 139 | +</tr> |
| 140 | +<tr> |
| 141 | +<td><img src="../../docs/images/DSAPerf2.png"/></td> |
| 142 | +<td><img src="../../docs/images/DSAPerf3.png"/></td> |
| 143 | +</tr> |
| 144 | +</table> |
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