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Move test mode to avoid error (#99)
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bethac07 authored May 3, 2024
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Expand Up @@ -182,8 +182,6 @@ When you are done developing your pipeline, you can exit the `'Test Mode'` by cl

> **AIM: use the nuclear channel to segment (isolate and identify all the pixels belonging to) each nuclei.**
- Enter '`Test Mode'` by clicking on <img src="./TutorialImages/startTestMode.png" width="120"/>.\

- Add an **IdentifyPrimaryObjects** module to the pipeline. Do this by clicking on the <img src="./TutorialImages/AddModule.png" width="35"/> button in the bottom left corner of the CellProfiler window, which will pop up a small window called `‘Add modules’`. Navigate to the `Object Processing` category and select **IdentifyPrimaryObjects**. Double click on the module or click on <img src="./TutorialImages/AddToPipeline.png" width="120"/>.

> **Tip**: You can also use the `'Find Modules'` search bar at the top of the ‘Add modules’ window to search all modules by name.
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- Adjust the threshold method, may lead to better (or worse!) results.
- Adjust the declumping settings.

- Enter '`Test Mode'` by clicking on <img src="./TutorialImages/startTestMode.png" width="120"/>.\

- Hit <img src="./TutorialImages/Step.png" width="120"/> after each change to rerun the module and see how the new parameters affect the segmentation.

- Adjust the segmentation parameters until you feel you’re ready to move on to identifying the cells around the nuclei.
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