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documents:120206pyip_cooking:python_imagej_cookbook [2017/12/03 06:08]
kota [Automatic Brightness/Contrast Button] human language explanation added
documents:120206pyip_cooking:python_imagej_cookbook [2018/08/19 18:32] (current)
kota [Channel Splitter]
Line 772: Line 772:
 imps[0].show() # Channel 1 imps[0].show() # Channel 1
 imps[1].show() # Channel 2 imps[1].show() # Channel 2
 +</​code>​
 +
 +==== Channel Merge ====
 +
 +[Image > Color > Merge Channels...]
 +
 +<code python linenums:​1>​
 +from ij import ImagePlus
 +from ij.plugin import RGBStackMerge,​ RGBStackConverter
 +
 +impc1 = ImagePlus("​path/​to/​image.tif"​)
 +impc2 = ImagePlus("​path/​to/​image.tif"​)
 +
 +mergeimp = RGBStackMerge.mergeChannels([impc2,​ None, impc1, None, None, None, None], True)
 +
 +# convert the composite image to the RGB image
 +RGBStackConverter.convertToRGB(mergeimp)
 +
 +mergeimp.show()
 </​code>​ </​code>​
 ==== Z projection ==== ==== Z projection ====
Line 1309: Line 1328:
  
 <code python linenums:​1>​ <code python linenums:​1>​
 +from ij import IJ, ImagePlus
 from ij.plugin.filter import ParticleAnalyzer as PA from ij.plugin.filter import ParticleAnalyzer as PA
 +from ij.measure import ResultsTable
 +
 imp = IJ.getImage() imp = IJ.getImage()
  
Line 1519: Line 1541:
 cm.setPointSize(3) cm.setPointSize(3)
 </​code>​ </​code>​
-===== Plugin: LOCI BioFormats, Replacing OME-TIFF XML =====+===== Plugin: LOCI BioFormats ​===== 
 + 
 +==== Importing CZI file ==== 
 + 
 +<code python linenums:​1>​ 
 +from loci.plugins import BF 
 +from loci.plugins.in import ImporterOptions 
 + 
 +filepath = "/​path/​to/​image/​my.czi"​ 
 + 
 +# Options for Bioformats pluginincludeing the image path 
 +options = ImporterOptions() 
 +options.setOpenAllSeries(True) 
 +options.setShowOMEXML(False) 
 +options.setStitchTiles(False) 
 +options.setId(filepath) 
 +     
 +fullimps = BF.openImagePlus(options) 
 + 
 +#fullimps now holds multiple images contained within the czi file.  
 +# open the first one.  
 +fullimps[0].show() 
 +</​code>​ 
 + 
 +See here for more on metadata parsing and so on: [[https://​gist.github.com/​ctrueden/​6282856|bio-formats.py]] 
 + 
 +==== Replacing OME-TIFF XML ====
  
 <code python linenums:​1>​ <code python linenums:​1>​
documents/120206pyip_cooking/python_imagej_cookbook.1512310080.txt.gz · Last modified: 2017/12/03 06:08 by kota