Hellow, I'm new to ImageJ.
I'm now trying to draw small 3D spheres or balls which have arbitrary radius and pixel values on DICOM images. I have searched 3D plugins but failed. Please let me know the way how to accomplish. Thanks in advance. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Hi,
Have a look to 3Dtools on wiki : http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_tools:start I am sure there are also some tools in Fiji. Best, Thomas > Hellow, I'm new to ImageJ. > I'm now trying to draw small 3D spheres or balls which have arbitrary > radius and pixel values on DICOM images. > I have searched 3D plugins but failed. > Please let me know the way how to accomplish. > Thanks in advance. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- Thomas Boudier, UPMC -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Dear Thomas
Thank you for yorur advice. I succeeded to draw a sphere on DICOM images. Can I ask one more question ? If I want to draw so many spheres on DICOM images, do i have to make a macro ? Thanks, Munemura 2014-04-16 12:00 GMT+09:00 Thomas Boudier <[hidden email]>: > Hi, > > Have a look to 3Dtools on wiki : > > http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_tools:start > > I am sure there are also some tools in Fiji. > > Best, > > Thomas > > > > > Hellow, I'm new to ImageJ. > > I'm now trying to draw small 3D spheres or balls which have arbitrary > > radius and pixel values on DICOM images. > > I have searched 3D plugins but failed. > > Please let me know the way how to accomplish. > > Thanks in advance. > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > > -- > Thomas Boudier, UPMC > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ★++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++★ 鈴木 宗村 *スズキ・メディカルイメージング・ラボ* 代表 放射線診断専門医 〒891-0141 鹿児島市谷山中央4丁目217-6パーレイⅡ205 Tel: 090-5923-6565 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Suzuki Munemura, MD * Suzuki Medical imaging Labo* President, radiologist 217-6-205, taniyamachuo, Kagoshima city, 891-0104 Japan Tel: +81-90-5923-6565 e-mail: [hidden email], [hidden email] ★+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++(^_^)+★ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Dear Munemura,
Yes, you will need to write a macro, you can use the one given as example : sx=256; sy=256; sz=256; nb=100; max_rad=16; min_rad=5; Dialog.create("Smarties 3D"); Dialog.addNumber("Number:", nb); Dialog.addNumber("SizeX:", sx); Dialog.addNumber("SizeY:", sy); Dialog.addNumber("SizeZ:", sz); Dialog.addNumber("Min_Radius:", min_rad); Dialog.addNumber("Max_Radius:", max_rad); Dialog.show(); nb = Dialog.getNumber(); sx = Dialog.getNumber(); sy = Dialog.getNumber(); sz = Dialog.getNumber(); min_rad = Dialog.getNumber(); max_rad = Dialog.getNumber(); newImage("Smarties", "16-bit Black", sx, sy, sz); for(i=1;i<=nb;i++) { cx=random*sx; cy=random*sy; cz=random*sz; rx=min_rad+random*(max_rad-min_rad); ry=min_rad+random*(max_rad-min_rad); rz=min_rad+random*(max_rad-min_rad); vx=random; vy=random; vz=random; wx=-vy; wy=vx; wz=0; val=i; run("3D Draw Shape", "size="+sx+","+sy+","+sz+" center="+cx+","+cy+","+cz+" radius="+rx+","+ry+","+rz+" vector1="+vx+","+vy+","+vz+" vector2="+wx+","+wy+","+wz+" res_xy=1.000 res_z=1.000 unit=pix value=&val display=Overwrite 3d_viewer"); call("ij3d.ImageJ3DViewer.select", "ellipsoid"+i); call("ij3d.ImageJ3DViewer.setColor", d2s(random*255,0), d2s(random*255,0), d2s(random*255,0)); } selectWindow("Smarties"); setSlice(nSlices/2); run("Enhance Contrast", "saturated=0"); run("3-3-2 RGB"); tell me if you need help writing the macro. best, Thomas > Dear Thomas > > Thank you for yorur advice. I succeeded to draw a sphere on DICOM images. > Can I ask one more question ? If I want to draw so many spheres on DICOM > images, do i have to make a macro ? > > Thanks, > > Munemura > > > 2014-04-16 12:00 GMT+09:00 Thomas Boudier <[hidden email]>: > >> Hi, >> >> Have a look to 3Dtools on wiki : >> >> http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_tools:start >> >> I am sure there are also some tools in Fiji. >> >> Best, >> >> Thomas >> >> >> >> > Hellow, I'm new to ImageJ. >> > I'm now trying to draw small 3D spheres or balls which have arbitrary >> > radius and pixel values on DICOM images. >> > I have searched 3D plugins but failed. >> > Please let me know the way how to accomplish. >> > Thanks in advance. >> > >> > -- >> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > >> > >> >> >> -- >> Thomas Boudier, UPMC >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > > > -- > â ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++â > é´æ¨ å®æ > *ã¹ãºãã»ã¡ãã£ã«ã«ã¤ã¡ã¼ã¸ã³ã°ã»ã©ã* > 代表 æ¾å°ç·è¨ºæå°éå» > ã891-0141 鹿å 島å¸è°·å±±ä¸å¤®4ä¸ç®217-6ãã¼ã¬ã¤â ¡205 > Tel: 090-5923-6565 > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > Suzuki Munemura, MD > * Suzuki Medical imaging Labo* > President, radiologist > 217-6-205, taniyamachuo, Kagoshima city, 891-0104 Japan > Tel: +81-90-5923-6565 > e-mail: [hidden email], [hidden email] > â +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++(^_^)+â > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- Thomas Boudier, UPMC -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
In reply to this post by Munemura Suzuki
Dear Thomas
Thank you for your quick reply. I undersatand i have to write a macro, but i have little knowledge about neither macro nor programing. The spheres I want to draw have the same size and pixel value. Can I draw the spheres just to point the center of the spheres one by one ? Or butch convert the file which have the cordinate data of center of the spheres ? If it would not be too much trouble, please give me advice. Thanks in advance Munemura 2014-04-16 15:39 GMT+09:00 Thomas Boudier <[hidden email]>: > Dear Munemura, > > Yes, you will need to write a macro, you can use the one given as example : > > sx=256; > sy=256; > sz=256; > > nb=100; > max_rad=16; > min_rad=5; > > Dialog.create("Smarties 3D"); > Dialog.addNumber("Number:", nb); > Dialog.addNumber("SizeX:", sx); > Dialog.addNumber("SizeY:", sy); > Dialog.addNumber("SizeZ:", sz); > Dialog.addNumber("Min_Radius:", min_rad); > Dialog.addNumber("Max_Radius:", max_rad); > Dialog.show(); > nb = Dialog.getNumber(); > sx = Dialog.getNumber(); > sy = Dialog.getNumber(); > sz = Dialog.getNumber(); > min_rad = Dialog.getNumber(); > max_rad = Dialog.getNumber(); > > newImage("Smarties", "16-bit Black", sx, sy, sz); > > for(i=1;i<=nb;i++) { > cx=random*sx; > cy=random*sy; > cz=random*sz; > rx=min_rad+random*(max_rad-min_rad); > ry=min_rad+random*(max_rad-min_rad); > rz=min_rad+random*(max_rad-min_rad); > vx=random; > vy=random; > vz=random; > wx=-vy; wy=vx; wz=0; > val=i; > > run("3D Draw Shape", "size="+sx+","+sy+","+sz+" > center="+cx+","+cy+","+cz+" radius="+rx+","+ry+","+rz+" > vector1="+vx+","+vy+","+vz+" vector2="+wx+","+wy+","+wz+" res_xy=1.000 > res_z=1.000 unit=pix value=&val display=Overwrite 3d_viewer"); > call("ij3d.ImageJ3DViewer.select", "ellipsoid"+i); > call("ij3d.ImageJ3DViewer.setColor", d2s(random*255,0), > d2s(random*255,0), d2s(random*255,0)); > } > > selectWindow("Smarties"); > setSlice(nSlices/2); > run("Enhance Contrast", "saturated=0"); > run("3-3-2 RGB"); > > > tell me if you need help writing the macro. > > best, > > Thomas > > > > Dear Thomas > > > > Thank you for yorur advice. I succeeded to draw a sphere on DICOM images. > > Can I ask one more question ? If I want to draw so many spheres on DICOM > > images, do i have to make a macro ? > > > > Thanks, > > > > Munemura > > > > > > 2014-04-16 12:00 GMT+09:00 Thomas Boudier <[hidden email] > >: > > > >> Hi, > >> > >> Have a look to 3Dtools on wiki : > >> > >> http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_tools:start > >> > >> I am sure there are also some tools in Fiji. > >> > >> Best, > >> > >> Thomas > >> > >> > >> > >> > Hellow, I'm new to ImageJ. > >> > I'm now trying to draw small 3D spheres or balls which have arbitrary > >> > radius and pixel values on DICOM images. > >> > I have searched 3D plugins but failed. > >> > Please let me know the way how to accomplish. > >> > Thanks in advance. > >> > > >> > -- > >> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > >> > > >> > > >> > >> > >> -- > >> Thomas Boudier, UPMC > >> > >> -- > >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > >> > > > > > > > > -- > > > ★++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++★ > > 鈴木 宗村 > > *スズキ・メディカルイメージング・ラボ* > > 代表 放射線診断専門医 > > 〒891-0141 鹿児島市谷山中央4丁目217-6パーレイⅡ205 > > Tel: 090-5923-6565 > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > > Suzuki Munemura, MD > > * Suzuki Medical imaging Labo* > > President, radiologist > > 217-6-205, taniyamachuo, Kagoshima city, 891-0104 Japan > > Tel: +81-90-5923-6565 > > e-mail: [hidden email], [hidden email] > > > ★+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++(^_^)+★ > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > > -- > Thomas Boudier, UPMC > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Hi,
Maybe you want to simply "point"some features in your 3D data, have a look to 3Dviewer and then use the "point" tool and clicks in 3D to the positions of interest. Best, Thomas > Dear Thomas > > Thank you for your quick reply. > I undersatand i have to write a macro, but i have little knowledge about > neither macro nor programing. > The spheres I want to draw have the same size and pixel value. Can I draw > the spheres just to point the center of the spheres one by one ? Or butch > convert the file which have the cordinate data of center of the spheres ? > If it would not be too much trouble, please give me advice. > Thanks in advance > > Munemura > > > > 2014-04-16 15:39 GMT+09:00 Thomas Boudier <[hidden email]>: > >> Dear Munemura, >> >> Yes, you will need to write a macro, you can use the one given as >> example : >> >> sx=256; >> sy=256; >> sz=256; >> >> nb=100; >> max_rad=16; >> min_rad=5; >> >> Dialog.create("Smarties 3D"); >> Dialog.addNumber("Number:", nb); >> Dialog.addNumber("SizeX:", sx); >> Dialog.addNumber("SizeY:", sy); >> Dialog.addNumber("SizeZ:", sz); >> Dialog.addNumber("Min_Radius:", min_rad); >> Dialog.addNumber("Max_Radius:", max_rad); >> Dialog.show(); >> nb = Dialog.getNumber(); >> sx = Dialog.getNumber(); >> sy = Dialog.getNumber(); >> sz = Dialog.getNumber(); >> min_rad = Dialog.getNumber(); >> max_rad = Dialog.getNumber(); >> >> newImage("Smarties", "16-bit Black", sx, sy, sz); >> >> for(i=1;i<=nb;i++) { >> cx=random*sx; >> cy=random*sy; >> cz=random*sz; >> rx=min_rad+random*(max_rad-min_rad); >> ry=min_rad+random*(max_rad-min_rad); >> rz=min_rad+random*(max_rad-min_rad); >> vx=random; >> vy=random; >> vz=random; >> wx=-vy; wy=vx; wz=0; >> val=i; >> >> run("3D Draw Shape", "size="+sx+","+sy+","+sz+" >> center="+cx+","+cy+","+cz+" radius="+rx+","+ry+","+rz+" >> vector1="+vx+","+vy+","+vz+" vector2="+wx+","+wy+","+wz+" res_xy=1.000 >> res_z=1.000 unit=pix value=&val display=Overwrite 3d_viewer"); >> call("ij3d.ImageJ3DViewer.select", "ellipsoid"+i); >> call("ij3d.ImageJ3DViewer.setColor", d2s(random*255,0), >> d2s(random*255,0), d2s(random*255,0)); >> } >> >> selectWindow("Smarties"); >> setSlice(nSlices/2); >> run("Enhance Contrast", "saturated=0"); >> run("3-3-2 RGB"); >> >> >> tell me if you need help writing the macro. >> >> best, >> >> Thomas >> >> >> > Dear Thomas >> > >> > Thank you for yorur advice. I succeeded to draw a sphere on DICOM >> images. >> > Can I ask one more question ? If I want to draw so many spheres on >> DICOM >> > images, do i have to make a macro ? >> > >> > Thanks, >> > >> > Munemura >> > >> > >> > 2014-04-16 12:00 GMT+09:00 Thomas Boudier >> <[hidden email] >> >: >> > >> >> Hi, >> >> >> >> Have a look to 3Dtools on wiki : >> >> >> >> http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_tools:start >> >> >> >> I am sure there are also some tools in Fiji. >> >> >> >> Best, >> >> >> >> Thomas >> >> >> >> >> >> >> >> > Hellow, I'm new to ImageJ. >> >> > I'm now trying to draw small 3D spheres or balls which have >> arbitrary >> >> > radius and pixel values on DICOM images. >> >> > I have searched 3D plugins but failed. >> >> > Please let me know the way how to accomplish. >> >> > Thanks in advance. >> >> > >> >> > -- >> >> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> > >> >> > >> >> >> >> >> >> -- >> >> Thomas Boudier, UPMC >> >> >> >> -- >> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> >> > >> > >> > >> > -- >> > >> â ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++â >> > é´æ¨ å®æ >> > *ã¹ãºãã»ã¡ãã£ã«ã«ã¤ã¡ã¼ã¸ã³ã°ã»ã©ã* >> > 代表 æ¾å°ç·è¨ºæå°éå» >> > ã891-0141 鹿å 島å¸è°·å±±ä¸å¤®4ä¸ç®217-6ãã¼ã¬ã¤â ¡205 >> > Tel: 090-5923-6565 >> > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >> > Suzuki Munemura, MD >> > * Suzuki Medical imaging Labo* >> > President, radiologist >> > 217-6-205, taniyamachuo, Kagoshima city, 891-0104 Japan >> > Tel: +81-90-5923-6565 >> > e-mail: [hidden email], [hidden email] >> > >> â +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++(^_^)+â >> > >> > -- >> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > >> > >> >> >> -- >> Thomas Boudier, UPMC >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- Thomas Boudier, UPMC -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Dear Thomas
That's what I wanted to do ! I have just tried. It seems the best method for my purpose. I appreciate all of your advice. Best regards, Munemura 2014-04-16 16:58 GMT+09:00 Thomas Boudier <[hidden email]>: > Hi, > > Maybe you want to simply "point"some features in your 3D data, have a look > to 3Dviewer and then use the "point" tool and clicks in 3D to the > positions of interest. > > Best, > > Thomas > > > > Dear Thomas > > > > Thank you for your quick reply. > > I undersatand i have to write a macro, but i have little knowledge about > > neither macro nor programing. > > The spheres I want to draw have the same size and pixel value. Can I draw > > the spheres just to point the center of the spheres one by one ? Or butch > > convert the file which have the cordinate data of center of the spheres ? > > If it would not be too much trouble, please give me advice. > > Thanks in advance > > > > Munemura > > > > > > > > 2014-04-16 15:39 GMT+09:00 Thomas Boudier <[hidden email] > >: > > > >> Dear Munemura, > >> > >> Yes, you will need to write a macro, you can use the one given as > >> example : > >> > >> sx=256; > >> sy=256; > >> sz=256; > >> > >> nb=100; > >> max_rad=16; > >> min_rad=5; > >> > >> Dialog.create("Smarties 3D"); > >> Dialog.addNumber("Number:", nb); > >> Dialog.addNumber("SizeX:", sx); > >> Dialog.addNumber("SizeY:", sy); > >> Dialog.addNumber("SizeZ:", sz); > >> Dialog.addNumber("Min_Radius:", min_rad); > >> Dialog.addNumber("Max_Radius:", max_rad); > >> Dialog.show(); > >> nb = Dialog.getNumber(); > >> sx = Dialog.getNumber(); > >> sy = Dialog.getNumber(); > >> sz = Dialog.getNumber(); > >> min_rad = Dialog.getNumber(); > >> max_rad = Dialog.getNumber(); > >> > >> newImage("Smarties", "16-bit Black", sx, sy, sz); > >> > >> for(i=1;i<=nb;i++) { > >> cx=random*sx; > >> cy=random*sy; > >> cz=random*sz; > >> rx=min_rad+random*(max_rad-min_rad); > >> ry=min_rad+random*(max_rad-min_rad); > >> rz=min_rad+random*(max_rad-min_rad); > >> vx=random; > >> vy=random; > >> vz=random; > >> wx=-vy; wy=vx; wz=0; > >> val=i; > >> > >> run("3D Draw Shape", "size="+sx+","+sy+","+sz+" > >> center="+cx+","+cy+","+cz+" radius="+rx+","+ry+","+rz+" > >> vector1="+vx+","+vy+","+vz+" vector2="+wx+","+wy+","+wz+" res_xy=1.000 > >> res_z=1.000 unit=pix value=&val display=Overwrite 3d_viewer"); > >> call("ij3d.ImageJ3DViewer.select", "ellipsoid"+i); > >> call("ij3d.ImageJ3DViewer.setColor", d2s(random*255,0), > >> d2s(random*255,0), d2s(random*255,0)); > >> } > >> > >> selectWindow("Smarties"); > >> setSlice(nSlices/2); > >> run("Enhance Contrast", "saturated=0"); > >> run("3-3-2 RGB"); > >> > >> > >> tell me if you need help writing the macro. > >> > >> best, > >> > >> Thomas > >> > >> > >> > Dear Thomas > >> > > >> > Thank you for yorur advice. I succeeded to draw a sphere on DICOM > >> images. > >> > Can I ask one more question ? If I want to draw so many spheres on > >> DICOM > >> > images, do i have to make a macro ? > >> > > >> > Thanks, > >> > > >> > Munemura > >> > > >> > > >> > 2014-04-16 12:00 GMT+09:00 Thomas Boudier > >> <[hidden email] > >> >: > >> > > >> >> Hi, > >> >> > >> >> Have a look to 3Dtools on wiki : > >> >> > >> >> http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_tools:start > >> >> > >> >> I am sure there are also some tools in Fiji. > >> >> > >> >> Best, > >> >> > >> >> Thomas > >> >> > >> >> > >> >> > >> >> > Hellow, I'm new to ImageJ. > >> >> > I'm now trying to draw small 3D spheres or balls which have > >> arbitrary > >> >> > radius and pixel values on DICOM images. > >> >> > I have searched 3D plugins but failed. > >> >> > Please let me know the way how to accomplish. > >> >> > Thanks in advance. > >> >> > > >> >> > -- > >> >> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > >> >> > > >> >> > > >> >> > >> >> > >> >> -- > >> >> Thomas Boudier, UPMC > >> >> > >> >> -- > >> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > >> >> > >> > > >> > > >> > > >> > -- > >> > > >> > ★++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++★ > >> > 鈴木 宗村 > >> > *スズキ・メディカルイメージング・ラボ* > >> > 代表 放射線診断専門医 > >> > 〒891-0141 鹿児島市谷山中央4丁目217-6パーレイⅡ205 > >> > Tel: 090-5923-6565 > >> > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > >> > Suzuki Munemura, MD > >> > * Suzuki Medical imaging Labo* > >> > President, radiologist > >> > 217-6-205, taniyamachuo, Kagoshima city, 891-0104 Japan > >> > Tel: +81-90-5923-6565 > >> > e-mail: [hidden email], [hidden email] > >> > > >> > ★+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++(^_^)+★ > >> > > >> > -- > >> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > >> > > >> > > >> > >> > >> -- > >> Thomas Boudier, UPMC > >> > >> -- > >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > >> > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > > -- > Thomas Boudier, UPMC > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ★++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++★ 鈴木 宗村 *スズキ・メディカルイメージング・ラボ* 代表 放射線診断専門医 〒891-0141 鹿児島市谷山中央4丁目217-6パーレイⅡ205 Tel: 090-5923-6565 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Suzuki Munemura, MD * Suzuki Medical imaging Labo* President, radiologist 217-6-205, taniyamachuo, Kagoshima city, 891-0104 Japan Tel: +81-90-5923-6565 e-mail: [hidden email], [hidden email] ★+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++(^_^)+★ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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