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change for docs
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marta-seq committed Jul 8, 2024
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6 changes: 3 additions & 3 deletions docs/source/notebook_usage.rst
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ Open the notebook and click Kernel -> Restart and Run all

For all channels in a stack it should look like this:

.. image:: figs\\all_ch_image.png
.. image:: ../../figs/all_ch_image.png
:alt: layout of the noteboook and folder structure for stacks of channels


Expand All @@ -31,7 +31,7 @@ set as index numbers.
In the case of directory with multiple files, the channel names should be in the file names.


.. image:: D:\\PycharmProjects\\phd\\Preprocess_IMC\\figs\\all_ch_image_2.png
.. image:: ../../figs/all_ch_image_2.png
:alt: layout of the noteboook with image comparison

Once you have the values for percentile and thresholds defined you can save your images by just clicking
Expand All @@ -43,7 +43,7 @@ channel at once.
In case of stacks with multiple channels per FOV, you need to define
the values per each channel in the pop up table and click save (see below).

.. image:: D:\\PycharmProjects\\phd\\Preprocess_IMC\\figs\\save_table.png
.. image:: ../../figs/save_table.png
:alt: saving table

Saving images will mimick your structure and filenames (and pagetags) in the
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