draw ROIs on different slices
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Hello everyone,
I wondered if ImageJ is able to draw ROIs on different slices and it also remembers the slice information. Currently it does not seems that ImageJ include the slice# information, all the ROIs basically are overlapped. Also not sure if ImageJ is able to make label images. Thanks for any hints. Ping -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: draw ROIs on different slices
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I suppose 'roi.setPosition(sliceNo)' is what you are looking for ...
--Wilhelm On Tue, Oct 13, 2020 at 4:49 AM Wang Ping <[hidden email]> wrote: > Hello everyone, > > I wondered if ImageJ is able to draw ROIs on different slices and it also > remembers the slice information. Currently it does not seems that ImageJ > include the slice# information, all the ROIs basically are overlapped. Also > not sure if ImageJ is able to make label images. > > Thanks for any hints. > Ping > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by WangPing
Dear Ping,
Check in the ROI Manager menu under More > Options if 'Associate "Show All" Rois with slices' is selected. I am not sure what you mean with your second question about label images. Best wishes Kees Dr Ir K.R. Straatman Advanced Imaging Facility University of Leicester www.le.ac.uk/advanced-imaging-facility<http://www.le.ac.uk/advanced-imaging-facility> ________________________________ From: Wang Ping <[hidden email]> Sent: 13 October 2020 03:48 To: [hidden email] <[hidden email]> Subject: draw ROIs on different slices Hello everyone, I wondered if ImageJ is able to draw ROIs on different slices and it also remembers the slice information. Currently it does not seems that ImageJ include the slice# information, all the ROIs basically are overlapped. Also not sure if ImageJ is able to make label images. Thanks for any hints. Ping -- ImageJ mailing list: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=02%7C01%7Ckrs5%40leicester.ac.uk%7C6df5029f721a4c64d35a08d86f228cff%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637381541472428945&sdata=x6uzNo18o9RJofPYgzN17mYPp7I232ro4xVa0jbfv1s%3D&reserved=0 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Kees,
Thank you so much for your email, For the first question, would it be possible to save the ROIs (drawn on different slices) into a mask image volume, with the slice information matching the original image volume? For the second question, I meant to see if it is possible to assign a different label to different ROI, for example, I draw one ROI and label all the pixels inside with "1", and another ROI with all pixels labeled with "2", this way I can recognize different ROIs. Thanks again, Ping ________________________________ 发件人: ImageJ Interest Group <[hidden email]> 代表 Straatman, Kees (Dr.) <[hidden email]> 发送时间: 2020年10月13日 16:23 收件人: [hidden email] <[hidden email]> 主题: Re: draw ROIs on different slices Dear Ping, Check in the ROI Manager menu under More > Options if 'Associate "Show All" Rois with slices' is selected. I am not sure what you mean with your second question about label images. Best wishes Kees Dr Ir K.R. Straatman Advanced Imaging Facility University of Leicester www.le.ac.uk/advanced-imaging-facility<http://www.le.ac.uk/advanced-imaging-facility<http://www.le.ac.uk/advanced-imaging-facility<http://www.le.ac.uk/advanced-imaging-facility>> ________________________________ From: Wang Ping <[hidden email]> Sent: 13 October 2020 03:48 To: [hidden email] <[hidden email]> Subject: draw ROIs on different slices Hello everyone, I wondered if ImageJ is able to draw ROIs on different slices and it also remembers the slice information. Currently it does not seems that ImageJ include the slice# information, all the ROIs basically are overlapped. Also not sure if ImageJ is able to make label images. Thanks for any hints. Ping -- ImageJ mailing list: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=02%7C01%7Ckrs5%40leicester.ac.uk%7C6df5029f721a4c64d35a08d86f228cff%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637381541472428945&sdata=x6uzNo18o9RJofPYgzN17mYPp7I232ro4xVa0jbfv1s%3D&reserved=0 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: 回复: draw ROIs on different slices
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Dear Ping,
For your second request, either you are programming in macro language and use the Roi.setProperty(key, value) and Roi.getProperty(key) methods: http://wsr.imagej.net/developer/macro/functions.html#R or in java and use the setProperty(java.lang.String key, java.lang.String value) and getProperty(java.lang.String property) methods: https://imagej.nih.gov/ij/developer/api/ij/gui/Roi.html My best regards, Philippe Philippe CARL Laboratoire de Bioimagerie et Pathologies UMR 7021 CNRS - Université de Strasbourg Faculté de Pharmacie 74 route du Rhin 67401 ILLKIRCH Tel : +33(0)3 68 85 42 89 ----- Mail original ----- De: "Wang Ping" <[hidden email]> À: "imagej" <[hidden email]> Envoyé: Mardi 13 Octobre 2020 16:30:36 Objet: 回复: draw ROIs on different slices Hi Kees, Thank you so much for your email, For the first question, would it be possible to save the ROIs (drawn on different slices) into a mask image volume, with the slice information matching the original image volume? For the second question, I meant to see if it is possible to assign a different label to different ROI, for example, I draw one ROI and label all the pixels inside with "1", and another ROI with all pixels labeled with "2", this way I can recognize different ROIs. Thanks again, Ping ________________________________ 发件人: ImageJ Interest Group <[hidden email]> 代表 Straatman, Kees (Dr.) <[hidden email]> 发送时间: 2020年10月13日 16:23 收件人: [hidden email] <[hidden email]> 主题: Re: draw ROIs on different slices Dear Ping, Check in the ROI Manager menu under More > Options if 'Associate "Show All" Rois with slices' is selected. I am not sure what you mean with your second question about label images. Best wishes Kees Dr Ir K.R. Straatman Advanced Imaging Facility University of Leicester www.le.ac.uk/advanced-imaging-facility<http://www.le.ac.uk/advanced-imaging-facility<http://www.le.ac.uk/advanced-imaging-facility<http://www.le.ac.uk/advanced-imaging-facility>> ________________________________ From: Wang Ping <[hidden email]> Sent: 13 October 2020 03:48 To: [hidden email] <[hidden email]> Subject: draw ROIs on different slices Hello everyone, I wondered if ImageJ is able to draw ROIs on different slices and it also remembers the slice information. Currently it does not seems that ImageJ include the slice# information, all the ROIs basically are overlapped. Also not sure if ImageJ is able to make label images. Thanks for any hints. Ping -- ImageJ mailing list: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=02%7C01%7Ckrs5%40leicester.ac.uk%7C6df5029f721a4c64d35a08d86f228cff%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637381541472428945&sdata=x6uzNo18o9RJofPYgzN17mYPp7I232ro4xVa0jbfv1s%3D&reserved=0 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by WangPing
Dear Ping, Would think so. One way that comes in mind is if you have the ROIs in the ROI Manager and create a new Z-tack with the same dimensions as your image you can add the ROIs to the new image and fill them (More > Fill) using a different colour than the new image. You cannot put a label inside a pixel, it is a single pixel, the smallest unit of your image. So, you cannot put something inside it. You can put a single label in each ROI being it the label number (just select Labels in the ROI Manager) or label name (select Labels and then go to More>Labels...). Best wishes Kees ________________________________ From: Wang Ping <[hidden email]> Sent: 13 October 2020 15:30 To: [hidden email] <[hidden email]> Cc: Straatman, Kees (Dr.) <[hidden email]> Subject: 回复: draw ROIs on different slices Hi Kees, Thank you so much for your email, For the first question, would it be possible to save the ROIs (drawn on different slices) into a mask image volume, with the slice information matching the original image volume? For the second question, I meant to see if it is possible to assign a different label to different ROI, for example, I draw one ROI and label all the pixels inside with "1", and another ROI with all pixels labeled with "2", this way I can recognize different ROIs. Thanks again, Ping ________________________________ 发件人: ImageJ Interest Group <[hidden email]> 代表 Straatman, Kees (Dr.) <[hidden email]> 发送时间: 2020年10月13日 16:23 收件人: [hidden email] <[hidden email]> 主题: Re: draw ROIs on different slices Dear Ping, Check in the ROI Manager menu under More > Options if 'Associate "Show All" Rois with slices' is selected. I am not sure what you mean with your second question about label images. Best wishes Kees Dr Ir K.R. Straatman Advanced Imaging Facility University of Leicester www.le.ac.uk/advanced-imaging-facility<http://www.le.ac.uk/advanced-imaging-facility<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.le.ac.uk%2Fadvanced-imaging-facility%253Chttp%3A%2F%2Fwww.le.ac.uk%2Fadvanced-imaging-facility&data=02%7C01%7Ckrs5%40LEICESTER.AC.UK%7Ca497378a02fb46f77e8e08d86f848e92%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637381962404536312&sdata=9T2jcc9pJ1s8OMy%2FgAhYD3nCGaB0kGLRx0OWoQfxcbE%3D&reserved=0>> ________________________________ From: Wang Ping <[hidden email]> Sent: 13 October 2020 03:48 To: [hidden email] <[hidden email]> Subject: draw ROIs on different slices Hello everyone, I wondered if ImageJ is able to draw ROIs on different slices and it also remembers the slice information. Currently it does not seems that ImageJ include the slice# information, all the ROIs basically are overlapped. Also not sure if ImageJ is able to make label images. Thanks for any hints. Ping -- ImageJ mailing list: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=02%7C01%7Ckrs5%40leicester.ac.uk%7C6df5029f721a4c64d35a08d86f228cff%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637381541472428945&sdata=x6uzNo18o9RJofPYgzN17mYPp7I232ro4xVa0jbfv1s%3D&reserved=0<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=02%7C01%7Ckrs5%40LEICESTER.AC.UK%7Ca497378a02fb46f77e8e08d86f848e92%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637381962404546306&sdata=TPS2m4y8t04fWV%2Ff57FNoe3HM66jq25h3CNfoQUDLXM%3D&reserved=0> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=02%7C01%7Ckrs5%40LEICESTER.AC.UK%7Ca497378a02fb46f77e8e08d86f848e92%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637381962404546306&sdata=TPS2m4y8t04fWV%2Ff57FNoe3HM66jq25h3CNfoQUDLXM%3D&reserved=0> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: »Ø¸´: draw ROIs on different slices
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In reply to this post by WangPing
Greetings Ping,
I assume that you are trying to create what I know as a map, i.e., a separate dataset that is conceptually the same as the original with the pixel values representing properties of the underlying pixel data - intended to use as a color overlay of the original data/image. If this is the case... With the source dataset current and no rois present, Image>Duplicate Process>Math>Set... (either nan or 0 or don't do by choice). Draw the roi on the source image then go to the map image and Ctrl-Shift-E. With the map dataset current Process>Math>Set... to the desired number. Repeat until happy. Note: 1) Set the display range appropriately for the map dataset or you will not detect your contrast. 2) The above works on a one roi on one slice at a time basis. I do not know how to do a distinct roi on each slice in one shot basis; this would be nice to know how to do. If my suspicion about you intentions are correct you may want to look into: https://imagej.net/Colorizer_Overlay Enjoy, Fred On Tue, October 13, 2020 9:30 am, Wang Ping wrote: > Hi Kees, > > Thank you so much for your email, > For the first question, would it be possible to save the ROIs (drawn on > different slices) into a mask image volume, with the slice information > matching the original image volume? > > For the second question, I meant to see if it is possible to assign a > different label to different ROI, for example, I draw one ROI and label > all the pixels inside with "1", and another ROI with all pixels labeled > with "2", this way I can recognize different ROIs. > > Thanks again, > Ping > > ________________________________ > ·¢¼þÈË: ImageJ Interest Group <[hidden email]> ´ú±í Straatman, Kees > (Dr.) <[hidden email]> > ·¢ËÍʱ¼ä: 2020Äê10ÔÂ13ÈÕ 16:23 > ÊÕ¼þÈË: [hidden email] <[hidden email]> > Ö÷Ìâ: Re: draw ROIs on different slices > > Dear Ping, > > Check in the ROI Manager menu under More > Options if 'Associate "Show > All" Rois with slices' is selected. > > I am not sure what you mean with your second question about label images. > > Best wishes > > Kees > > > Dr Ir K.R. Straatman > Advanced Imaging Facility > > University of Leicester > www.le.ac.uk/advanced-imaging-facility<http://www.le.ac.uk/advanced-imaging-facility<http://www.le.ac.uk/advanced-imaging-facility<http://www.le.ac.uk/advanced-imaging-facility>> > > > ________________________________ > From: Wang Ping <[hidden email]> > Sent: 13 October 2020 03:48 > To: [hidden email] <[hidden email]> > Subject: draw ROIs on different slices > > Hello everyone, > > I wondered if ImageJ is able to draw ROIs on different slices and it also > remembers the slice information. Currently it does not seems that ImageJ > include the slice# information, all the ROIs basically are overlapped. > Also not sure if ImageJ is able to make label images. > > Thanks for any hints. > Ping > > -- > ImageJ mailing list: > https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=02%7C01%7Ckrs5%40leicester.ac.uk%7C6df5029f721a4c64d35a08d86f228cff%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637381541472428945&sdata=x6uzNo18o9RJofPYgzN17mYPp7I232ro4xVa0jbfv1s%3D&reserved=0 > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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