Setting custom measurement for scale bar in use for measuring fungal spores and other microscopic details of fungi
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Setting custom measurement for scale bar in use for measuring fungal spores and other microscopic details of fungi
 
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>>> I am new to ImageJ and have been trying utilise the programme to set up my own scale bar set to 10 microns, to be able to measure fungal spore with it. I have already photographed the scale bar at a x1000 on my microscope and have opened it in ImageJ. I was able to create a 10micron scale bar for comparing an spores against but I need the exact measurements to actually appear when I measure the spores. Would it be possible for somebody to please clearly explain the process that I need to follow, to be able to achieve this?
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Setting custom measurement for scale bar in use for measuring fungal spores and other microscopic details of fungi
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Hi Andy,
there are several web pages explaining how to set the image scale; some of these even have a link in the ImageJ documentation: http://rsbweb.nih.gov/ij/docs/guide/146-30.html#toc-Subsection-30.8 Others are e.g. http://microscopy.berkeley.edu/courses/dib/sections/04IPIII/IJsetscale.html http://serc.carleton.edu/eyesinthesky2/week2/get_to_know_imagej.html#find_scale http://skepticwonder.fieldofscience.com/2009/11/quick-imagej-tutorial-scalebar.html http://wiki.imagej.net/SpatialCalibration And any internet search engine will give you dozens of others... Michael ________________________________________________________________ On Jul 25, 2014, at 17:17, Andy Overall wrote: > I am new to ImageJ and have been trying utilise the programme to set up my own scale bar set to 10 microns, to be able to measure fungal spore with it. I have already photographed the scale bar at a x1000 on my microscope and have opened it in ImageJ. I was able to create a 10micron scale bar for comparing an spores against but I need the exact measurements to actually appear when I measure the spores. Would it be possible for somebody to please clearly explain the process that I need to follow, to be able to achieve this? -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Setting custom measurement for scale bar in use for measuring fungal spores and other microscopic details of fungi
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Thanks Michael,
Hopefully I can pull something together form one of these options, sure its not that difficult but the process can be a tad convoluted..... Thanks again Andy On 25 Jul 2014, at 17:39, Michael Schmid wrote: > Hi Andy, > > there are several web pages explaining how to set the image scale; some of these even have a link in the ImageJ documentation: > http://rsbweb.nih.gov/ij/docs/guide/146-30.html#toc-Subsection-30.8 > > Others are e.g. > http://microscopy.berkeley.edu/courses/dib/sections/04IPIII/IJsetscale.html > http://serc.carleton.edu/eyesinthesky2/week2/get_to_know_imagej.html#find_scale > http://skepticwonder.fieldofscience.com/2009/11/quick-imagej-tutorial-scalebar.html > http://wiki.imagej.net/SpatialCalibration > > And any internet search engine will give you dozens of others... > > Michael > ________________________________________________________________ > > > On Jul 25, 2014, at 17:17, Andy Overall wrote: > >> I am new to ImageJ and have been trying utilise the programme to set up my own scale bar set to 10 microns, to be able to measure fungal spore with it. I have already photographed the scale bar at a x1000 on my microscope and have opened it in ImageJ. I was able to create a 10micron scale bar for comparing an spores against but I need the exact measurements to actually appear when I measure the spores. Would it be possible for somebody to please clearly explain the process that I need to follow, to be able to achieve this? > > -- > 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 Michael Schmid
Dear Andy,
Once you have a scaled image you can use the straight line Tool to draw a line from one side of the spore to the other. Press 'm' and you should see a result appearing. Repeat to do more measurements. You can deselect everything under Analyze > Set Measurements and the results will only show you Angle and Length of your line. Good luck Kees -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Michael Schmid Sent: 25 July 2014 17:39 To: [hidden email] Subject: Re: Setting custom measurement for scale bar in use for measuring fungal spores and other microscopic details of fungi Hi Andy, there are several web pages explaining how to set the image scale; some of these even have a link in the ImageJ documentation: http://rsbweb.nih.gov/ij/docs/guide/146-30.html#toc-Subsection-30.8 Others are e.g. http://microscopy.berkeley.edu/courses/dib/sections/04IPIII/IJsetscale.html http://serc.carleton.edu/eyesinthesky2/week2/get_to_know_imagej.html#find_scale http://skepticwonder.fieldofscience.com/2009/11/quick-imagej-tutorial-scalebar.html http://wiki.imagej.net/SpatialCalibration And any internet search engine will give you dozens of others... Michael ________________________________________________________________ On Jul 25, 2014, at 17:17, Andy Overall wrote: > I am new to ImageJ and have been trying utilise the programme to set up my own scale bar set to 10 microns, to be able to measure fungal spore with it. I have already photographed the scale bar at a x1000 on my microscope and have opened it in ImageJ. I was able to create a 10micron scale bar for comparing an spores against but I need the exact measurements to actually appear when I measure the spores. Would it be possible for somebody to please clearly explain the process that I need to follow, to be able to achieve this? -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Setting custom measurement for scale bar in use for measuring fungal spores and other microscopic details of fungi
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Thanks Kees,
Yes, when I was trying measure the spore, that is exactly what I seeing, just angle and length. When you say scaled image......I assume that is following having managed to set up my scale, measurement, which is what I was having a problem doing. Once I have managed to this, then I shall try what you say. Many Thanks Andy On 25 Jul 2014, at 17:53, Straatman, Kees (Dr.) wrote: > Dear Andy, > > Once you have a scaled image you can use the straight line Tool to draw a line from one side of the spore to the other. Press 'm' and you should see a result appearing. Repeat to do more measurements. You can deselect everything under Analyze > Set Measurements and the results will only show you Angle and Length of your line. > > Good luck > > Kees > > > > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Michael Schmid > Sent: 25 July 2014 17:39 > To: [hidden email] > Subject: Re: Setting custom measurement for scale bar in use for measuring fungal spores and other microscopic details of fungi > > Hi Andy, > > there are several web pages explaining how to set the image scale; some of these even have a link in the ImageJ documentation: > http://rsbweb.nih.gov/ij/docs/guide/146-30.html#toc-Subsection-30.8 > > Others are e.g. > http://microscopy.berkeley.edu/courses/dib/sections/04IPIII/IJsetscale.html > http://serc.carleton.edu/eyesinthesky2/week2/get_to_know_imagej.html#find_scale > http://skepticwonder.fieldofscience.com/2009/11/quick-imagej-tutorial-scalebar.html > http://wiki.imagej.net/SpatialCalibration > > And any internet search engine will give you dozens of others... > > Michael > ________________________________________________________________ > > > On Jul 25, 2014, at 17:17, Andy Overall wrote: > >> I am new to ImageJ and have been trying utilise the programme to set up my own scale bar set to 10 microns, to be able to measure fungal spore with it. I have already photographed the scale bar at a x1000 on my microscope and have opened it in ImageJ. I was able to create a 10micron scale bar for comparing an spores against but I need the exact measurements to actually appear when I measure the spores. Would it be possible for somebody to please clearly explain the process that I need to follow, to be able to achieve this? > > -- > 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: Setting custom measurement for scale bar in use for measuring fungal spores and other microscopic details of fungi
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In reply to this post by Krs5
Thanks Kees,
I'm up and running I love the way that all of the measurements are kept in the pop up box, would I also be able to ascertain average sizes for say 20 spores and obtain a Q value? Thanks Andy On 25 Jul 2014, at 17:53, Straatman, Kees (Dr.) wrote: > Dear Andy, > > Once you have a scaled image you can use the straight line Tool to draw a line from one side of the spore to the other. Press 'm' and you should see a result appearing. Repeat to do more measurements. You can deselect everything under Analyze > Set Measurements and the results will only show you Angle and Length of your line. > > Good luck > > Kees > > > > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Michael Schmid > Sent: 25 July 2014 17:39 > To: [hidden email] > Subject: Re: Setting custom measurement for scale bar in use for measuring fungal spores and other microscopic details of fungi > > Hi Andy, > > there are several web pages explaining how to set the image scale; some of these even have a link in the ImageJ documentation: > http://rsbweb.nih.gov/ij/docs/guide/146-30.html#toc-Subsection-30.8 > > Others are e.g. > http://microscopy.berkeley.edu/courses/dib/sections/04IPIII/IJsetscale.html > http://serc.carleton.edu/eyesinthesky2/week2/get_to_know_imagej.html#find_scale > http://skepticwonder.fieldofscience.com/2009/11/quick-imagej-tutorial-scalebar.html > http://wiki.imagej.net/SpatialCalibration > > And any internet search engine will give you dozens of others... > > Michael > ________________________________________________________________ > > > On Jul 25, 2014, at 17:17, Andy Overall wrote: > >> I am new to ImageJ and have been trying utilise the programme to set up my own scale bar set to 10 microns, to be able to measure fungal spore with it. I have already photographed the scale bar at a x1000 on my microscope and have opened it in ImageJ. I was able to create a 10micron scale bar for comparing an spores against but I need the exact measurements to actually appear when I measure the spores. Would it be possible for somebody to please clearly explain the process that I need to follow, to be able to achieve this? > > -- > 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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Dear Andy,
If you right mouse-click in the results table you get several option including "Summarize" what will add Mean, SD, Min and Max to your results table, no Q-value. Is this Q-value related to FDR or something else? Best wishes Kees -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Andy Overall Sent: 26 July 2014 09:34 To: [hidden email] Subject: Re: Setting custom measurement for scale bar in use for measuring fungal spores and other microscopic details of fungi Thanks Kees, I'm up and running I love the way that all of the measurements are kept in the pop up box, would I also be able to ascertain average sizes for say 20 spores and obtain a Q value? Thanks Andy On 25 Jul 2014, at 17:53, Straatman, Kees (Dr.) wrote: > Dear Andy, > > Once you have a scaled image you can use the straight line Tool to draw a line from one side of the spore to the other. Press 'm' and you should see a result appearing. Repeat to do more measurements. You can deselect everything under Analyze > Set Measurements and the results will only show you Angle and Length of your line. > > Good luck > > Kees > > > > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > Michael Schmid > Sent: 25 July 2014 17:39 > To: [hidden email] > Subject: Re: Setting custom measurement for scale bar in use for > measuring fungal spores and other microscopic details of fungi > > Hi Andy, > > there are several web pages explaining how to set the image scale; some of these even have a link in the ImageJ documentation: > http://rsbweb.nih.gov/ij/docs/guide/146-30.html#toc-Subsection-30.8 > > Others are e.g. > http://microscopy.berkeley.edu/courses/dib/sections/04IPIII/IJsetscale > .html > http://serc.carleton.edu/eyesinthesky2/week2/get_to_know_imagej.html#f > ind_scale > http://skepticwonder.fieldofscience.com/2009/11/quick-imagej-tutorial- > scalebar.html http://wiki.imagej.net/SpatialCalibration > > And any internet search engine will give you dozens of others... > > Michael > ________________________________________________________________ > > > On Jul 25, 2014, at 17:17, Andy Overall wrote: > >> I am new to ImageJ and have been trying utilise the programme to set up my own scale bar set to 10 microns, to be able to measure fungal spore with it. I have already photographed the scale bar at a x1000 on my microscope and have opened it in ImageJ. I was able to create a 10micron scale bar for comparing an spores against but I need the exact measurements to actually appear when I measure the spores. Would it be possible for somebody to please clearly explain the process that I need to follow, to be able to achieve this? > > -- > 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: Setting custom measurement for scale bar in use for measuring fungal spores and other microscopic details of fungi
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Thanks Kees,
Very helpful. The Q value is the ratio of length/breadth for a single spores and the observed range of the ratio of length/breadth for all spores measured. Best Andy On 28 Jul 2014, at 08:47, Straatman, Kees (Dr.) wrote: > Dear Andy, > > If you right mouse-click in the results table you get several option including "Summarize" what will add Mean, SD, Min and Max to your results table, no Q-value. Is this Q-value related to FDR or something else? > > Best wishes > > Kees > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Andy Overall > Sent: 26 July 2014 09:34 > To: [hidden email] > Subject: Re: Setting custom measurement for scale bar in use for measuring fungal spores and other microscopic details of fungi > > Thanks Kees, > > I'm up and running I love the way that all of the measurements are kept in the pop up box, would I also be able to ascertain average sizes for say 20 spores and obtain a Q value? > > Thanks > > Andy > > On 25 Jul 2014, at 17:53, Straatman, Kees (Dr.) wrote: > >> Dear Andy, >> >> Once you have a scaled image you can use the straight line Tool to draw a line from one side of the spore to the other. Press 'm' and you should see a result appearing. Repeat to do more measurements. You can deselect everything under Analyze > Set Measurements and the results will only show you Angle and Length of your line. >> >> Good luck >> >> Kees >> >> >> >> -----Original Message----- >> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of >> Michael Schmid >> Sent: 25 July 2014 17:39 >> To: [hidden email] >> Subject: Re: Setting custom measurement for scale bar in use for >> measuring fungal spores and other microscopic details of fungi >> >> Hi Andy, >> >> there are several web pages explaining how to set the image scale; some of these even have a link in the ImageJ documentation: >> http://rsbweb.nih.gov/ij/docs/guide/146-30.html#toc-Subsection-30.8 >> >> Others are e.g. >> http://microscopy.berkeley.edu/courses/dib/sections/04IPIII/IJsetscale >> .html >> http://serc.carleton.edu/eyesinthesky2/week2/get_to_know_imagej.html#f >> ind_scale >> http://skepticwonder.fieldofscience.com/2009/11/quick-imagej-tutorial- >> scalebar.html http://wiki.imagej.net/SpatialCalibration >> >> And any internet search engine will give you dozens of others... >> >> Michael >> ________________________________________________________________ >> >> >> On Jul 25, 2014, at 17:17, Andy Overall wrote: >> >>> I am new to ImageJ and have been trying utilise the programme to set up my own scale bar set to 10 microns, to be able to measure fungal spore with it. I have already photographed the scale bar at a x1000 on my microscope and have opened it in ImageJ. I was able to create a 10micron scale bar for comparing an spores against but I need the exact measurements to actually appear when I measure the spores. Would it be possible for somebody to please clearly explain the process that I need to follow, to be able to achieve this? >> >> -- >> 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 |
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