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docs/source/notebook_usage.rst

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@@ -11,7 +11,7 @@ Open the notebook and click Kernel -> Restart and Run all
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For all channels in a stack it should look like this:
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.. image:: figs\\all_ch_image.png
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.. image:: ../../figs/all_ch_image.png
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:alt: layout of the noteboook and folder structure for stacks of channels
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In the case of directory with multiple files, the channel names should be in the file names.
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.. image:: D:\\PycharmProjects\\phd\\Preprocess_IMC\\figs\\all_ch_image_2.png
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.. image:: ../../figs/all_ch_image_2.png
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:alt: layout of the noteboook with image comparison
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Once you have the values for percentile and thresholds defined you can save your images by just clicking
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In case of stacks with multiple channels per FOV, you need to define
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the values per each channel in the pop up table and click save (see below).
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.. image:: D:\\PycharmProjects\\phd\\Preprocess_IMC\\figs\\save_table.png
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.. image:: ../../figs/save_table.png
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:alt: saving table
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Saving images will mimick your structure and filenames (and pagetags) in the

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