Re: Counting cells using Image J
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Re: Counting cells using Image J
 
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Hi everyone,
I will like to count cells from Alcian blue staining using image J. I have tried following the steps plugin >analyse> cell counter and it does not work. Could anyone tell me what to do? Thanks Bridget -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Oceane Sent: April-27-16 10:19 AM To: [hidden email] Subject: Counting structures within measured ROI Dear all, I am new to Image J and and I am slowly starting to realize the levels of complexity it offers. I want to measure several ROIs in my picture, and manually count cells only within those who have a minor/major axis ratio >0.85. I tried using the freehand selection tool and measurement command, but I can't seem to link the ROIs to the measurement, select the ones that are round enough, and then link my cell count to one particular ROI. Is there a way for me to produce a single table containing the ROI measurements and the structure count ? Thanks a LOT for your help! Océane -- View this message in context: http://imagej.1557.x6.nabble.com/Counting-structures-within-measured-ROI-tp5016248.html Sent from the ImageJ mailing list archive at Nabble.com. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Counting cells using Image J
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Hi Bridget,
At what point do you encounter the problems with cell counter? This question may be stupid, but did you initialize your image for counting? Best, Chris Christian Renicke, M.Sc. Ph.D. Student University of Marburg - Department of Biology Group of Prof. Dr. H.U. Mösch - Junior Group of Dr. C. Taxis Karl-von-Frisch Str. 8 D-35043 Marburg Phone: +49 6421 / 2823246 E-Mail: [hidden email] Am 27.04.2016 um 17:09 schrieb Fomenky, Bridget: > Hi everyone, > > I will like to count cells from Alcian blue staining using image J. I have tried following the steps plugin >analyse> cell counter and it does not work. > Could anyone tell me what to do? > > Thanks > > Bridget > > > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Oceane > Sent: April-27-16 10:19 AM > To: [hidden email] > Subject: Counting structures within measured ROI > > Dear all, > I am new to Image J and and I am slowly starting to realize the levels of complexity it offers. > I want to measure several ROIs in my picture, and manually count cells only within those who have a minor/major axis ratio >0.85. > I tried using the freehand selection tool and measurement command, but I can't seem to link the ROIs to the measurement, select the ones that are round enough, and then link my cell count to one particular ROI. > Is there a way for me to produce a single table containing the ROI measurements and the structure count ? > Thanks a LOT for your help! > Océane > > > > -- > View this message in context: http://imagej.1557.x6.nabble.com/Counting-structures-within-measured-ROI-tp5016248.html > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > 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 |
Re: Counting cells using Image J
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Hi Christine,
Yes I did try to initialize but I am not able to initialize. Is there a particular thing I need to do to be able to initialize? Bridget -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Christian Renicke Sent: April-27-16 12:17 PM To: [hidden email] Subject: Re: Counting cells using Image J Hi Bridget, At what point do you encounter the problems with cell counter? This question may be stupid, but did you initialize your image for counting? Best, Chris Christian Renicke, M.Sc. Ph.D. Student University of Marburg - Department of Biology Group of Prof. Dr. H.U. Mösch - Junior Group of Dr. C. Taxis Karl-von-Frisch Str. 8 D-35043 Marburg Phone: +49 6421 / 2823246 E-Mail: [hidden email] Am 27.04.2016 um 17:09 schrieb Fomenky, Bridget: > Hi everyone, > > I will like to count cells from Alcian blue staining using image J. I have tried following the steps plugin >analyse> cell counter and it does not work. > Could anyone tell me what to do? > > Thanks > > Bridget > > > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > Oceane > Sent: April-27-16 10:19 AM > To: [hidden email] > Subject: Counting structures within measured ROI > > Dear all, > I am new to Image J and and I am slowly starting to realize the levels of complexity it offers. > I want to measure several ROIs in my picture, and manually count cells only within those who have a minor/major axis ratio >0.85. > I tried using the freehand selection tool and measurement command, but I can't seem to link the ROIs to the measurement, select the ones that are round enough, and then link my cell count to one particular ROI. > Is there a way for me to produce a single table containing the ROI measurements and the structure count ? > Thanks a LOT for your help! > Océane > > > > -- > View this message in context: > http://imagej.1557.x6.nabble.com/Counting-structures-within-measured-R > OI-tp5016248.html Sent from the ImageJ mailing list archive at > Nabble.com. > > -- > 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 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Fomenky, Bridget
Hi
I don't have experience on using cell counter but I know "analyze -- analyze particles" are good for 2D object counting and "analyze -- 3D object counter" are good for 3D object counting. Possibility these function will work for you. Best Jiyuan Kang On Wed, Apr 27, 2016 at 11:09 AM, Fomenky, Bridget < [hidden email]> wrote: > Hi everyone, > > I will like to count cells from Alcian blue staining using image J. I > have tried following the steps plugin >analyse> cell counter and it does > not work. > Could anyone tell me what to do? > > Thanks > > Bridget > > > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > Oceane > Sent: April-27-16 10:19 AM > To: [hidden email] > Subject: Counting structures within measured ROI > > Dear all, > I am new to Image J and and I am slowly starting to realize the levels of > complexity it offers. > I want to measure several ROIs in my picture, and manually count cells > only within those who have a minor/major axis ratio >0.85. > I tried using the freehand selection tool and measurement command, but I > can't seem to link the ROIs to the measurement, select the ones that are > round enough, and then link my cell count to one particular ROI. > Is there a way for me to produce a single table containing the ROI > measurements and the structure count ? > Thanks a LOT for your help! > Océane > > > > -- > View this message in context: > http://imagej.1557.x6.nabble.com/Counting-structures-within-measured-ROI-tp5016248.html > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > 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 |
Re: Counting cells using Image J
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Hi Jiyuang,
I will also try that and let you know ASAP. Thanks Bridget -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jiyuan Kang Sent: April-27-16 1:22 PM To: [hidden email] Subject: Re: Counting cells using Image J Hi I don't have experience on using cell counter but I know "analyze -- analyze particles" are good for 2D object counting and "analyze -- 3D object counter" are good for 3D object counting. Possibility these function will work for you. Best Jiyuan Kang On Wed, Apr 27, 2016 at 11:09 AM, Fomenky, Bridget < [hidden email]> wrote: > Hi everyone, > > I will like to count cells from Alcian blue staining using image J. I > have tried following the steps plugin >analyse> cell counter and it does > not work. > Could anyone tell me what to do? > > Thanks > > Bridget > > > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > Oceane > Sent: April-27-16 10:19 AM > To: [hidden email] > Subject: Counting structures within measured ROI > > Dear all, > I am new to Image J and and I am slowly starting to realize the levels > of complexity it offers. > I want to measure several ROIs in my picture, and manually count cells > only within those who have a minor/major axis ratio >0.85. > I tried using the freehand selection tool and measurement command, but > I can't seem to link the ROIs to the measurement, select the ones that > are round enough, and then link my cell count to one particular ROI. > Is there a way for me to produce a single table containing the ROI > measurements and the structure count ? > Thanks a LOT for your help! > Océane > > > > -- > View this message in context: > http://imagej.1557.x6.nabble.com/Counting-structures-within-measured-R > OI-tp5016248.html Sent from the ImageJ mailing list archive at > Nabble.com. > > -- > 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 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Counting cells using Image J
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In reply to this post by Fomenky, Bridget
Two important things you have not mention, are the cells individually visible, that is are they all separated by some background, at least a couple of pixels. If not you will need to process with a watershed, or an open or close operation. Secondly you didn't mention of you thresholded your cells, that have to sufficiently distinct from background so that you end up with a binary image - cells foreground, everything else background.
Mike -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Fomenky, Bridget Sent: Wednesday, April 27, 2016 11:10 AM To: [hidden email] Subject: Re: Counting cells using Image J Hi everyone, I will like to count cells from Alcian blue staining using image J. I have tried following the steps plugin >analyse> cell counter and it does not work. Could anyone tell me what to do? Thanks Bridget -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Oceane Sent: April-27-16 10:19 AM To: [hidden email] Subject: Counting structures within measured ROI Dear all, I am new to Image J and and I am slowly starting to realize the levels of complexity it offers. I want to measure several ROIs in my picture, and manually count cells only within those who have a minor/major axis ratio >0.85. I tried using the freehand selection tool and measurement command, but I can't seem to link the ROIs to the measurement, select the ones that are round enough, and then link my cell count to one particular ROI. Is there a way for me to produce a single table containing the ROI measurements and the structure count ? Thanks a LOT for your help! Océane -- View this message in context: http://imagej.1557.x6.nabble.com/Counting-structures-within-measured-ROI-tp5016248.html Sent from the ImageJ mailing list archive at Nabble.com. -- 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 |
Re: Counting cells using Image J
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Hi Mike,
The cells are individually visible. I am new to image J I do not know what you mean by threshold of the cells . Thanks Bridget -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Mike Esterman Sent: April-27-16 2:36 PM To: [hidden email] Subject: Re: Counting cells using Image J Two important things you have not mention, are the cells individually visible, that is are they all separated by some background, at least a couple of pixels. If not you will need to process with a watershed, or an open or close operation. Secondly you didn't mention of you thresholded your cells, that have to sufficiently distinct from background so that you end up with a binary image - cells foreground, everything else background. Mike -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Fomenky, Bridget Sent: Wednesday, April 27, 2016 11:10 AM To: [hidden email] Subject: Re: Counting cells using Image J Hi everyone, I will like to count cells from Alcian blue staining using image J. I have tried following the steps plugin >analyse> cell counter and it does not work. Could anyone tell me what to do? Thanks Bridget -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Oceane Sent: April-27-16 10:19 AM To: [hidden email] Subject: Counting structures within measured ROI Dear all, I am new to Image J and and I am slowly starting to realize the levels of complexity it offers. I want to measure several ROIs in my picture, and manually count cells only within those who have a minor/major axis ratio >0.85. I tried using the freehand selection tool and measurement command, but I can't seem to link the ROIs to the measurement, select the ones that are round enough, and then link my cell count to one particular ROI. Is there a way for me to produce a single table containing the ROI measurements and the structure count ? Thanks a LOT for your help! Océane -- View this message in context: http://imagej.1557.x6.nabble.com/Counting-structures-within-measured-ROI-tp5016248.html Sent from the ImageJ mailing list archive at Nabble.com. -- 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 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Counting cells using Image J
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Bridget
If you have an RGB image, since you mentioned the cells were stained with Alcian Blue I would separate into the Red Green and Blue color planes. You do this with Image menu / Color / Split Channels now you have a gray scale image. To Threshold: again Image menu / Adjust / Threshold You will have a window with a histogram and slider bars underneath. If your background is bright then make sure the checkbox for Dark Background is unchecked. Looking at the image play with the upper and lower sliders until the cells are filled with red and the background is unchanged then select apply. Now you have a binary image with the cells black and the background white. Then you can use the Analyze menu and Analyze particles. Since you are new to image J I suggest you get on the image or the FIJI web site and go through the on line manual it is pretty good tutorial to get you started. Also I would suggest John Russ's book "The Image Processing Handbook" it is available on Amazon. Get an older edition much cheaper. Mike -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Fomenky, Bridget Sent: Wednesday, April 27, 2016 4:46 PM To: [hidden email] Subject: Re: Counting cells using Image J Hi Mike, The cells are individually visible. I am new to image J I do not know what you mean by threshold of the cells . Thanks Bridget -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Mike Esterman Sent: April-27-16 2:36 PM To: [hidden email] Subject: Re: Counting cells using Image J Two important things you have not mention, are the cells individually visible, that is are they all separated by some background, at least a couple of pixels. If not you will need to process with a watershed, or an open or close operation. Secondly you didn't mention of you thresholded your cells, that have to sufficiently distinct from background so that you end up with a binary image - cells foreground, everything else background. Mike -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Fomenky, Bridget Sent: Wednesday, April 27, 2016 11:10 AM To: [hidden email] Subject: Re: Counting cells using Image J Hi everyone, I will like to count cells from Alcian blue staining using image J. I have tried following the steps plugin >analyse> cell counter and it does not work. Could anyone tell me what to do? Thanks Bridget -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Oceane Sent: April-27-16 10:19 AM To: [hidden email] Subject: Counting structures within measured ROI Dear all, I am new to Image J and and I am slowly starting to realize the levels of complexity it offers. I want to measure several ROIs in my picture, and manually count cells only within those who have a minor/major axis ratio >0.85. I tried using the freehand selection tool and measurement command, but I can't seem to link the ROIs to the measurement, select the ones that are round enough, and then link my cell count to one particular ROI. Is there a way for me to produce a single table containing the ROI measurements and the structure count ? Thanks a LOT for your help! Océane -- View this message in context: http://imagej.1557.x6.nabble.com/Counting-structures-within-measured-ROI-tp5016248.html Sent from the ImageJ mailing list archive at Nabble.com. -- 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 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Counting cells using Image J
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In reply to this post by Fomenky, Bridget
> On Apr 27, 2016, at 1:22 PM, Fomenky, Bridget <[hidden email]> wrote:
> > Hi Christine, > > Yes I did try to initialize but I am not able to initialize. Is there a particular thing I need to do to be able to initialize? There is no need to initialize the image if you use the built-in multi-point tool to do the counting instead of the Cell Counter plugin. Double click on the multi-point tool icon and click “Help” for more information. You will need to be running ImageJ 1.50d or later. -wayne > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Christian Renicke > Sent: April-27-16 12:17 PM > To: [hidden email] > Subject: Re: Counting cells using Image J > > Hi Bridget, > > At what point do you encounter the problems with cell counter? This question may be stupid, but did you initialize your image for counting? > > Best, > > Chris > > Christian Renicke, M.Sc. > Ph.D. Student > University of Marburg - Department of Biology Group of Prof. Dr. H.U. Mösch - Junior Group of Dr. C. Taxis Karl-von-Frisch Str. 8 > D-35043 Marburg > > Phone: +49 6421 / 2823246 > E-Mail: [hidden email] > > Am 27.04.2016 um 17:09 schrieb Fomenky, Bridget: >> Hi everyone, >> >> I will like to count cells from Alcian blue staining using image J. I have tried following the steps plugin >analyse> cell counter and it does not work. >> Could anyone tell me what to do? >> >> Thanks >> >> Bridget >> >> >> -----Original Message----- >> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of >> Oceane >> Sent: April-27-16 10:19 AM >> To: [hidden email] >> Subject: Counting structures within measured ROI >> >> Dear all, >> I am new to Image J and and I am slowly starting to realize the levels of complexity it offers. >> I want to measure several ROIs in my picture, and manually count cells only within those who have a minor/major axis ratio >0.85. >> I tried using the freehand selection tool and measurement command, but I can't seem to link the ROIs to the measurement, select the ones that are round enough, and then link my cell count to one particular ROI. >> Is there a way for me to produce a single table containing the ROI measurements and the structure count ? >> Thanks a LOT for your help! >> Océane >> >> >> >> -- >> View this message in context: >> http://imagej.1557.x6.nabble.com/Counting-structures-within-measured-R >> OI-tp5016248.html Sent from the ImageJ mailing list archive at >> Nabble.com. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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