You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Copy file name to clipboardExpand all lines: docs/source/Data_analysis/Graphical_User_Interface.rst
+5-5Lines changed: 5 additions & 5 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -45,7 +45,7 @@ You can load more than one dataset to a Group, or have multiple Groups to visual
45
45
When more than one dataset is loaded, you cannot change the analysis parameters anymore.
46
46
In this mode, the analysis results are read-only.
47
47
The same parameters should be used to comparing different datasets.
48
-
To make sure that the chosen parameters work with each dataset, load each one separately and verify the peak detection first.
48
+
To make sure that the chosen parameters are appropriate for each dataset, load each one separately and verify the peak detection first.
49
49
The comparison plots in the Plot menu will show results by Group.
50
50
In the upper left corner of the GUI, a dropdown menu can be used to change the Group that is currently being visualized.
51
51
@@ -81,7 +81,7 @@ The ``emb_numbers.png`` file represents a snapshot of the microscope's field of
81
81
Config parameters
82
82
-----------------
83
83
84
-
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.
84
+
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.
85
85
If not found, a file with default parameters is created.
86
86
The default parameters can be found inside ``config.py``.
87
87
If you change any of the parameters, they will be recorded in this file.
@@ -95,7 +95,7 @@ From this window it's possible to set:
95
95
* Group name: name of the group that contains this dataset
96
96
* 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.
97
97
* To_exclude: embryo numbers that will be excluded from the analysis. These embryos will be excluded from the analysis.
98
-
* To_remove: embryo numbers that will be analyzed, but will show up in the 'Removed' group.
98
+
* To_remove: embryo numbers that will be analyzed, but will appear in the 'Removed' group.
99
99
* 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.
100
100
* Has_transients: if selected the code will try to identify and skip the first peak if it's likely just a transient.
101
101
* Has_dsna: if selected the code will try to determine dSNA and ignore all peaks that happen after dSNA start.
@@ -109,8 +109,8 @@ Visualizing traces
109
109
110
110
The description here refers to the image on the top of the file.
111
111
112
-
The top app bar has buttons to change the data presentation.
113
-
Below the top app bar there are two sliders.
112
+
The top bar has buttons to change the data presentation.
113
+
Below the top bar there are two sliders.
114
114
The first is for the frequency cutoff, which controls how much the signal is smoothed for the finding peaks algorithm.
115
115
The second is the peak width parameter, used to determine the start and end times of each peak.
116
116
The sidebar presents which embryos are currently considered for plots and analysis, and which ones should be removed.
0 commit comments