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Say I have 4 image plus objects open. how would I close 3 of them, without
closing the one I want? To try and do this, I find that if I do the following they all close and when the want I want to open again pops up, all the pixels are white ImagePlus keep = WindowManager.getImage(firstImageID); ImageProcessor i = keep.getProcessor(); WindowManager.closeAllWindows(); new ImagePlus("",i).show(); |
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Hello,
I have several multi-colour confocal images with a slight x-y-shift between the channels. As a first step before re-align the system, is there a plugin or a macro that allows me to correct this shift? It would mean to shift a layer for a defined number of pixels. Thanks in advance, Michael |
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> I have several multi-colour confocal images with a slight x-y-shift
> between the channels. As a first step before re-align the system, > is there a plugin or a macro that allows me to correct this shift? > It would mean to shift a layer for a defined number of pixels. Here is a macro that shifts the red, green or blue channel in an RGB image by a specified number of pixels. -wayne if (bitDepth!=24 || nSlices!=1) exit("RGB Image required"); Dialog.create("RGB Shift"); Dialog.addChoice("Channel:", newArray("Red", "Green", "Blue")); Dialog.addNumber("X Shift:", 10); Dialog.addNumber("Y Shift:", 10); Dialog.addCheckbox("Create New Image", true); Dialog.show(); xshift = Dialog.getNumber(); yshift = Dialog.getNumber(); channel = Dialog.getChoice(); create = Dialog.getCheckbox(); setBatchMode(true); if (create) { setKeyDown("alt"); run("Duplicate..."); } run("RGB Stack"); if (channel=="Green") setSlice(2); else if (channel=="Blue") setSlice(3); run("Select All"); setBackgroundColor(0, 0, 0); run("Cut"); makeRectangle(xshift, yshift, getWidth, getHeight); run("Paste"); run("RGB Color"); setBatchMode(false); |
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In reply to this post by Michael Weber-4
> I have several multi-colour confocal images with a slight x-y-shift
> between the channels. As a first step before re-align the system, > is there a plugin or a macro that allows me to correct this shift? > It would mean to shift a layer for a defined number of pixels. I misread the message and missed the "channels" bit. I thought it was asking for a registration/stitching plugins (which there are a few in the IJ site). The plugin Align_RGB_planes may also help: http://www.dentistry.bham.ac.uk/landinig/software/software.html Cheers. G. |
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The align_rgb plugin works fine as is exactly what I was looking for.
thanks, Michael >> I have several multi-colour confocal images with a slight x-y-shift >> between the channels. As a first step before re-align the system, >> is there a plugin or a macro that allows me to correct this shift? >> It would mean to shift a layer for a defined number of pixels. > > I misread the message and missed the "channels" bit. I thought it was > asking > for a registration/stitching plugins (which there are a few in the IJ > site). > > The plugin Align_RGB_planes may also help: > > http://www.dentistry.bham.ac.uk/landinig/software/software.html > > Cheers. > > G. > ... [show rest of quote] __________________________ Michael Weber (B.Sc.) MPI-CBG Dresden, Light Microscopy Facility phone: +49 351 2102837 |
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