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--- documents:120206pyip_cooking:python_imagej_cookbook [2017/12/03 14:08] – [Automatic Brightness/Contrast Button] human language explanation added kota
+++ documents:120206pyip_cooking:python_imagej_cookbook [2018/08/20 01:32] – [Channel Splitter] kota
@@ Line 772: / Line 772: @@
 imps[0].show() # Channel 1
 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>
 ==== Z projection ====
@@ Line 1309: / Line 1328: @@
 <code python linenums:1>
+from ij import IJ, ImagePlus
 from ij.plugin.filter import ParticleAnalyzer as PA
+from ij.measure import ResultsTable
 imp = IJ.getImage()
@@ Line 1519: / Line 1541: @@
 cm.setPointSize(3)
 </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 plugin, includeing 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>