Analysis_ILM.nb

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Cell[CellGroupData[{
Cell["Analysis of Inverted Light Microscope Images", "Title",
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Cell["\<\
Last updated 06/01/16 by Leanne Friedrich
This notebook is for processing groups of images of printed lines, where \
particles are dark and the matrix and background are light. 
These images should be sorted into folders, which the ILM interface should do \
on its own. 
Images should start with ILM and end with .tif\
\>", "Text",
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Cell[CellGroupData[{

Cell["Initialization", "Chapter",
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Cell["\<\
Initialization will give you a variable called directories, which will be a \
list of sample folders in the directory where you saved this notebook. \
\>", "Text",
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Cell[CellGroupData[{

Cell["Checking for errors", "Chapter",
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Cell["\<\
Before running any analysis, you should check to see what your segmented \
images will look like. To do so, use ILMInterface. This will create an \
interface where you can input an index of a file in directories, and it will \
show all ILM images in that folder, and what they look like when the \
particles are segmented out. If you decide that a file is too bad to repair, \
use the buttons to delete it. The image will stay showing when you press the \
button, but you only need to press it once. For analysis, the program will \
only use the first 7 images. \
\>", "Text",
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Cell[CellGroupData[{

Cell["Analysis", "Chapter",
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Cell["\<\
To analyse images, use getAllImageStats[file, critical intensity for \
segmenting pixels, critical intensity for segmenting neighboring pixels]
getAllImageStats will just print out the directory name. If you want to \
identify problems, you must use ILM interface to see what the segmented \
images look like. \
\>", "Text",
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Cell["\<\
If you want to know what the composite profile looks like for a sample, use \
getILMProfile[the name of the directory]\
\>", "Text",
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