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Sensitivity versus resistance fix
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Add a fix for a ‘devision by zero’ situation
Normal notebook function now evaluates sensitive and resistance in colony growth equally unless the ‘onlysensitive’ flag is set to True in which case colony growth will be measured relative to the control and growth can never be more that the control.
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@marcvdijk
marcvdijk committed May 7, 2017
1 parent 3d42549 commit 2c9de27
Showing 1 changed file with 79 additions and 51 deletions.
130 changes: 79 additions & 51 deletions spot_assay_processor.nb
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Original file line number Diff line number Diff line change
Expand Up @@ -10,10 +10,10 @@
NotebookFileLineBreakTest
NotebookFileLineBreakTest
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WindowFrame->Normal*)

(* Beginning of Notebook Content *)
Expand Down Expand Up @@ -187,11 +187,11 @@ to process and optionally a reference image using a common system file \
selection dialog. You can test the script by using the test images shipped \
with the software (condition-x.png and the reference image control.png). \
Mathematica will handle most common image file formats automatically.\n\nOf \
the 3 program parameters you can set (",
the 4 program parameters you can set (",
StyleBox["imagegrid",
FontSlant->"Italic"],
", ",
StyleBox["padding",
StyleBox["padding, partionpadding",
FontSlant->"Italic"],
" and ",
StyleBox["tophatr",
Expand All @@ -202,12 +202,18 @@ the 3 program parameters you can set (",
" needs to match the grid layout of the colonies in your image as columns x \
rows. For the test images you need to set this parameter to {4, 12}. Please \
note that all the images you process in one run of the script need to have \
the same grid layout.\n\nThe program outputs a bar graph with a sensitivity \
value between 0 and 1 for every row in each of the images you supplied. In \
addition the sensitivity data for all images are exported to an Excel .xls \
file names \[OpenCurlyDoubleQuote]spottingdata.xls\[CloseCurlyDoubleQuote] by \
default in the same location as where the spot_assay_processor.nb notebook is \
located. The path to this file is defined in the ",
the same grid layout.\nIn case one is only interested in measuring \
sensitivity in colony growth that set the ",
StyleBox["onlysensitive",
FontSlant->"Italic"],
" parameter to true. All growth rates will be relative to the control where \
a test can never grow more than the control. \n\nThe program outputs a bar \
graph with a sensitivity value between 0 and 1 for every row in each of the \
images you supplied. In addition the sensitivity data for all images are \
exported to an Excel .xls file names \[OpenCurlyDoubleQuote]spottingdata.xls\
\[CloseCurlyDoubleQuote] by default in the same location as where the \
spot_assay_processor.nb notebook is located. The path to this file is defined \
in the ",
StyleBox["outputexcelpath",
FontSlant->"Italic"],
" variable.\n"
Expand All @@ -217,7 +223,9 @@ located. The path to this file is defined in the ",
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Cell[TextData[StyleBox["Program settings", "Section"]], "Text",
CellChangeTimes->{
Expand All @@ -233,9 +241,15 @@ Cell[BoxData[{
RowBox[{
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RowBox[{
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Expand Down Expand Up @@ -334,14 +348,11 @@ Cell[BoxData[{
RowBox[{
RowBox[{
RowBox[{"imagegrid", "[",
RowBox[{"[", "2", "]"}], "]"}], " ", "-", " ", "padding"}], ";"}], " ",

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RowBox[{"Function", "[",
RowBox[{"img", ",", "\[IndentingNewLine]",
Expand All @@ -352,7 +363,8 @@ Cell[BoxData[{
RowBox[{
RowBox[{"ImageDimensions", "[", "img", "]"}], "/", "imagegrid"}],
",", " ",
RowBox[{"Padding", "\[Rule]", "Black"}]}], " ", "]"}], ",", " ",
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RowBox[{"(*",
Expand Down Expand Up @@ -389,7 +401,19 @@ Cell[BoxData[{
RowBox[{"PartitionAndCount", "[",
RowBox[{"ProcessImage", "[",
RowBox[{"Import", "[", "controlimagepath", "]"}], "]"}], "]"}]}],
"]"}]}], ";"}], "\[IndentingNewLine]"}], "\[IndentingNewLine]",
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Expand Down Expand Up @@ -432,20 +456,22 @@ Cell[BoxData[{
"\[IndentingNewLine]",
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RowBox[{"If", " ", "onlysensitive"}], ",", " ",
RowBox[{
"Replace", " ", "all", " ", "normalized", " ", "count", " ",
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Expand All @@ -454,14 +480,13 @@ Cell[BoxData[{
RowBox[{"no", " ", "growth"}], ")"}]}], "*)"}], "\[IndentingNewLine]",
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Expand Down Expand Up @@ -701,7 +726,10 @@ Cell[BoxData[{
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CellChangeTimes->{3.675575702073803*^9},
Expand Down Expand Up @@ -732,7 +760,7 @@ Cell[BoxData[""], "Input",
NumberMarks->False]
},
WindowSize->{1043, 646},
WindowMargins->{{21, Automatic}, {Automatic, 12}},
WindowMargins->{{Automatic, 19}, {Automatic, 38}},
FrontEndVersion->"11.0 for Mac OS X x86 (32-bit, 64-bit Kernel) (July 28, \
2016)",
StyleDefinitions->"Default.nb"
Expand Down Expand Up @@ -767,14 +795,14 @@ Cell[7143, 158, 824, 13, 30, "Item"]
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*)
Expand Down

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