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docs: text review
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docs/source/Data_analysis/Graphical_User_Interface.rst

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@@ -45,7 +45,7 @@ You can load more than one dataset to a Group, or have multiple Groups to visual
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When more than one dataset is loaded, you cannot change the analysis parameters anymore.
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In this mode, the analysis results are read-only.
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The same parameters should be used to comparing different datasets.
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To make sure that the chosen parameters work with each dataset, load each one separately and verify the peak detection first.
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To make sure that the chosen parameters are appropriate for each dataset, load each one separately and verify the peak detection first.
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The comparison plots in the Plot menu will show results by Group.
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In the upper left corner of the GUI, a dropdown menu can be used to change the Group that is currently being visualized.
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@@ -81,7 +81,7 @@ The ``emb_numbers.png`` file represents a snapshot of the microscope's field of
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Config parameters
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-----------------
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When loading a dataset the code will look for a config file named ``peak_detection_params.json`` inside th dataset directory and will use its data for the analysis.
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When loading a dataset the code will look for a config file named ``peak_detection_params.json`` inside the dataset directory and will use its data for the analysis.
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If not found, a file with default parameters is created.
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The default parameters can be found inside ``config.py``.
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If you change any of the parameters, they will be recorded in this file.
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* Group name: name of the group that contains this dataset
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* First peak threshold: minimum time in minutes that has to pass before any peak happens. Used to make sure that the first peak caught at the imaging session is really the activity onset.
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* To_exclude: embryo numbers that will be excluded from the analysis. These embryos will be excluded from the analysis.
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* To_remove: embryo numbers that will be analyzed, but will show up in the 'Removed' group.
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* To_remove: embryo numbers that will be analyzed, but will appear in the 'Removed' group.
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* Embryos that have it's first peak before the first peak threshold or that were marked by the user as removed will also be at the to_remove category.
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* Has_transients: if selected the code will try to identify and skip the first peak if it's likely just a transient.
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* Has_dsna: if selected the code will try to determine dSNA and ignore all peaks that happen after dSNA start.
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The description here refers to the image on the top of the file.
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The top app bar has buttons to change the data presentation.
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Below the top app bar there are two sliders.
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The top bar has buttons to change the data presentation.
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Below the top bar there are two sliders.
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The first is for the frequency cutoff, which controls how much the signal is smoothed for the finding peaks algorithm.
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The second is the peak width parameter, used to determine the start and end times of each peak.
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The sidebar presents which embryos are currently considered for plots and analysis, and which ones should be removed.

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