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Segmentation

2,666 bytes added, 12:01, 26 April 2013
Add a brief walkthrough for segmentation workflows
More precisely, image segmentation is the process of ''assigning a label'' to every pixel in an image such that pixels with the same label share certain visual characteristics.
 
= Easy workflow =
 
One option which is designed to be very powerful, yet easy to use for non-experts in image processing:
 
<font size="5">&lt; [[Advanced Weka Segmentation]] &gt;</font>
 
Give it a try—you might like it!
 
= Flexible workflow =
 
One good workflow for segmentation in ImageJ is as follows:
 
# Preprocess the image using filters, to make later thresholding more effective. Which filter(s) to use is highly dependent on your data, but some commonly useful filters include:
#* [[:Category:Deconvolution|Deconvolution]]
#* [http://imagej.net/docs/guide/146-29.html#sub:Subtract-Background... Subtract Background]
#* [http://imagej.net/docs/guide/146-29.html#sub:Gaussian-Blur... Gaussian Blur]
#* [http://imagej.net/docs/guide/146-29.html#sub:Find-Edges Find Edges]
# Apply a [http://imagej.net/docs/guide/146-28.html#sub:Threshold...%5BT%5D Threshold].
#* Ideally you want to use one of the auto-threshold methods, rather than manually tweaking, so that your result is reproducible later on the same data, and on multiple other datasets.
# [http://imagej.net/docs/guide/146-29.html#infobox:InvertedLutMask Create a mask].
# Manipulate the mask as needed; e.g.:
#* [http://imagej.net/docs/guide/146-29.html#sub:Dilate Dilate] to grow the included pixels
#* [http://imagej.net/docs/guide/146-29.html#sub:Erode Erode] to shrink the included pixels
# [http://imagej.net/docs/guide/146-27.html#sub:Create-Selection Create a selection] from the mask.
# [http://imagej.net/docs/guide/146-27.html#infobox:TransferSelections Transfer the selection] back to your original image with the original (non-processed) pixel data.
#* If you ran filters on your data, you probably want to [http://imagej.net/docs/guide/146-26.html#sub:Revert%5Br%5D Revert] those changes first.
# Do some numerical analysis on the selected data; e.g.:
#* [http://imagej.net/docs/guide/146-30.html#sub:Measure...%5Bm%5D Measure] the entire selection directly.
#** Control which measurements are done using [http://imagej.nih.gov/ij/docs/guide/146-30.html#sub:Set-Measurements... Set Measurements].
#* Use [http://imagej.nih.gov/ij/docs/guide/146-30.html#sub:Analyze-Particles... Analyze Particles] to extract desirable objects from your selection and report individual statistics on them.
#* Use the [http://imagej.net/docs/guide/146-30.html#fig:The-ROI-Manager ROI Manager] to '''Add''' the selection and then '''Split''' it (under the '''More''' button), then use '''Multi Measure''' (also under '''More''') to report statistics on the objects.
#* [[Macros_Intro|Write a macro]] to automate this sort of analysis, loop over objects in the ROI manager, measure and manipulate them, etc.
= See also =
For a list of Fiji plugins which perform image segmentation, see: [[:Category:Segmentation]].
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