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lines changed Original file line number Diff line number Diff line change @@ -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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@@ -31,7 +31,7 @@ set as index numbers.
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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
@@ -43,7 +43,7 @@ channel at once.
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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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