Combining two max projection images with a 'transparency sliding rule'?
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Combining two max projection images with a 'transparency sliding rule'?
 
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Hi.
I have a stack of confocal images. As I go through the z axis, some structures appear that are partially covered by some overlaying surface. I did two partial maximum projection and would like to create a single image showing the whole structure. As the intensity of the first max proj is higher than the second, composing both is not a good solution. I remember that there was a software that combined two images and with a sliding rule one could vary the 'transparency of either image and get a good solution. My question is: is there any plugin with something similar to a 'transparency sliding rule' in Fiji/ImageJ? Thank you in advance for any help. Best Antonio -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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activate the ClearVolume plugin [Help/Update/Manage Update Sites; check
clearvolume]. It has ability to toggle channels on/off, plus opacity sliders per color. [clearvolume is fussy about graphics cards, however] cheers, Vytas On 8/18/2017 7:44 AM, Antonio G. Valdecasas wrote: > Hi. > > I have a stack of confocal images. As I go through the z axis, some > structures appear that are partially covered by some overlaying surface. > > I did two partial maximum projection and would like to create a single > image showing the whole structure. As the intensity of the first max proj > is higher than the second, composing both is not a good solution. > > I remember that there was a software that combined two images and with a > sliding rule one could vary the 'transparency of either image and get a > good solution. > > My question is: is there any plugin with something similar to a > 'transparency sliding rule' in Fiji/ImageJ? > > Thank you in advance for any help. > > Best > > Antonio > > -- > ImageJ mailing list: https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwIBaQ&c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzytxHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=X2ujGcA0wkKFUzrUxOYhSPJhlxE1YBB0JMY2MnVIYd8&s=GbOuUPPLmrvK-l6iYCsXxtwBNFwTcwYJeMPd6M6RT-s&e= -- __ Vytas Bindokas, Ph.D. Research Assoc. Prof., Director, BSD Light Microscopy Core Facility phone: 773-702-4875 [alt's: 773-834-9040 or 773-834-2639] [address for letters ONLY (see shipping addr below):] Dept Pharmacol Physiol Sci MC0926 947 E 58th Street The University of Chicago Chicago IL 60637 Room Abbott 129 shipping address (main KCBD site): V. Bindokas 900 E 57th Street KCBD room 1250, Microscopy Core The University of Chicago Chicago IL 60637 email [hidden email] web site for LMCF: http://digital.uchicago.edu -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Combining two max projection images with a 'transparency sliding rule'?
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Thank you very much, Vytas.
However, my version of Fiji/ImageJ 'Help >Update' does not leads to 'Manage Update Sites'. I have updated the Fiji/ImageJ version from a link in ClearVolume webpage with same result. Looking at the ClearVolume page I realize that the instalation of this plugin is a bit more complex than simply downloading a *.jar file in the plugin folder. Any additonal help would be greatly appreciated. Best Antonio 2017-08-18 16:23 GMT+02:00 vbindokas <[hidden email]>: > activate the ClearVolume plugin [Help/Update/Manage Update Sites; check > clearvolume]. > > It has ability to toggle channels on/off, plus opacity sliders per color. > > [clearvolume is fussy about graphics cards, however] > > cheers, > > Vytas > > > > On 8/18/2017 7:44 AM, Antonio G. Valdecasas wrote: > >> Hi. >> >> I have a stack of confocal images. As I go through the z axis, some >> structures appear that are partially covered by some overlaying surface. >> >> I did two partial maximum projection and would like to create a single >> image showing the whole structure. As the intensity of the first max proj >> is higher than the second, composing both is not a good solution. >> >> I remember that there was a software that combined two images and with a >> sliding rule one could vary the 'transparency of either image and get a >> good solution. >> >> My question is: is there any plugin with something similar to a >> 'transparency sliding rule' in Fiji/ImageJ? >> >> Thank you in advance for any help. >> >> Best >> >> Antonio >> >> -- >> ImageJ mailing list: https://urldefense.proofpoint. >> com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwIBaQ&c >> =Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzy >> txHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=X2ujGcA0wkKFUzrUxOYhSPJh >> lxE1YBB0JMY2MnVIYd8&s=GbOuUPPLmrvK-l6iYCsXxtwBNFwTcwYJeMPd6M6RT-s&e= >> > > -- > __ > > Vytas Bindokas, Ph.D. > Research Assoc. Prof., > Director, BSD Light Microscopy Core Facility > phone: 773-702-4875 [alt's: 773-834-9040 or 773-834-2639] > > [address for letters ONLY (see shipping addr below):] > Dept Pharmacol Physiol Sci MC0926 > 947 E 58th Street > The University of Chicago > Chicago IL 60637 > Room Abbott 129 > > > shipping address (main KCBD site): > V. Bindokas > 900 E 57th Street > KCBD room 1250, Microscopy Core > The University of Chicago > Chicago IL 60637 > > > email [hidden email] > web site for LMCF: > http://digital.uchicago.edu > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Antonio,
> However, my version of Fiji/ImageJ 'Help >Update' does not leads to > 'Manage Update Sites'. Are you sure you are choosing "Update..." and not "Update ImageJ..."? Did you read the documentation? https://imagej.net/Following_an_update_site#Add_update_sites > Looking at the ClearVolume page I realize that the instalation of > this plugin is a bit more complex than simply downloading a *.jar file > in the plugin folder. It is six clicks: * Help * Update... * "Manage Update Sites" button * "ClearVolume" checkbox * Close button * "Apply changes" button Regards, Curtis -- Curtis Rueden LOCI software architect - https://loci.wisc.edu/software ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you know ImageJ has a forum? http://forum.imagej.net/ On Sat, Aug 19, 2017 at 11:10 AM, Antonio G. Valdecasas <[hidden email]> wrote: > Thank you very much, Vytas. > > However, my version of Fiji/ImageJ 'Help >Update' does not > leads to 'Manage > Update Sites'. I have updated the Fiji/ImageJ version from a link in > ClearVolume webpage with same result. > > Looking at the ClearVolume page I realize that the instalation of this > plugin is a bit more complex than simply downloading a *.jar file in the > plugin folder. > > Any additonal help would be greatly appreciated. > > Best > > Antonio > > 2017-08-18 16:23 GMT+02:00 vbindokas <[hidden email]>: > > > activate the ClearVolume plugin [Help/Update/Manage Update Sites; check > > clearvolume]. > > > > It has ability to toggle channels on/off, plus opacity sliders per color. > > > > [clearvolume is fussy about graphics cards, however] > > > > cheers, > > > > Vytas > > > > > > > > On 8/18/2017 7:44 AM, Antonio G. Valdecasas wrote: > > > >> Hi. > >> > >> I have a stack of confocal images. As I go through the z axis, some > >> structures appear that are partially covered by some overlaying surface. > >> > >> I did two partial maximum projection and would like to create a single > >> image showing the whole structure. As the intensity of the first max > proj > >> is higher than the second, composing both is not a good solution. > >> > >> I remember that there was a software that combined two images and with a > >> sliding rule one could vary the 'transparency of either image and get a > >> good solution. > >> > >> My question is: is there any plugin with something similar to a > >> 'transparency sliding rule' in Fiji/ImageJ? > >> > >> Thank you in advance for any help. > >> > >> Best > >> > >> Antonio > >> > >> -- > >> ImageJ mailing list: https://urldefense.proofpoint. > >> com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwIBaQ&c > >> =Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzy > >> txHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=X2ujGcA0wkKFUzrUxOYhSPJh > >> lxE1YBB0JMY2MnVIYd8&s=GbOuUPPLmrvK-l6iYCsXxtwBNFwTcwYJeMPd6M6RT-s&e= > >> > > > > -- > > __ > > > > Vytas Bindokas, Ph.D. > > Research Assoc. Prof., > > Director, BSD Light Microscopy Core Facility > > phone: 773-702-4875 [alt's: 773-834-9040 or 773-834-2639] > > > > [address for letters ONLY (see shipping addr below):] > > Dept Pharmacol Physiol Sci MC0926 > > 947 E 58th Street > > The University of Chicago > > Chicago IL 60637 > > Room Abbott 129 > > > > > > shipping address (main KCBD site): > > V. Bindokas > > 900 E 57th Street > > KCBD room 1250, Microscopy Core > > The University of Chicago > > Chicago IL 60637 > > > > > > email [hidden email] > > web site for LMCF: > > http://digital.uchicago.edu > > > > -- > > 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: Combining two max projection images with a 'transparency sliding rule'?
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Thank you very much, Curtis.
I had overlooked the 'Manage Update Site' button at the left down corner!! Best Antonio 2017-08-20 13:03 GMT+02:00 Curtis Rueden <[hidden email]>: > Hi Antonio, > > > However, my version of Fiji/ImageJ 'Help >Update' does not leads to > > 'Manage Update Sites'. > > Are you sure you are choosing "Update..." and not "Update ImageJ..."? > > Did you read the documentation? > https://imagej.net/Following_an_update_site#Add_update_sites > > > Looking at the ClearVolume page I realize that the instalation of > > this plugin is a bit more complex than simply downloading a *.jar file > > in the plugin folder. > > It is six clicks: > > * Help > * Update... > * "Manage Update Sites" button > * "ClearVolume" checkbox > * Close button > * "Apply changes" button > > Regards, > Curtis > > > -- > Curtis Rueden > LOCI software architect - https://loci.wisc.edu/software > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden > Did you know ImageJ has a forum? http://forum.imagej.net/ > > > On Sat, Aug 19, 2017 at 11:10 AM, Antonio G. Valdecasas <[hidden email] > > > wrote: > > > Thank you very much, Vytas. > > > > However, my version of Fiji/ImageJ 'Help >Update' does not > > leads to 'Manage > > Update Sites'. I have updated the Fiji/ImageJ version from a link in > > ClearVolume webpage with same result. > > > > Looking at the ClearVolume page I realize that the instalation of this > > plugin is a bit more complex than simply downloading a *.jar file in the > > plugin folder. > > > > Any additonal help would be greatly appreciated. > > > > Best > > > > Antonio > > > > 2017-08-18 16:23 GMT+02:00 vbindokas <[hidden email]>: > > > > > activate the ClearVolume plugin [Help/Update/Manage Update Sites; check > > > clearvolume]. > > > > > > It has ability to toggle channels on/off, plus opacity sliders per > color. > > > > > > [clearvolume is fussy about graphics cards, however] > > > > > > cheers, > > > > > > Vytas > > > > > > > > > > > > On 8/18/2017 7:44 AM, Antonio G. Valdecasas wrote: > > > > > >> Hi. > > >> > > >> I have a stack of confocal images. As I go through the z axis, some > > >> structures appear that are partially covered by some overlaying > surface. > > >> > > >> I did two partial maximum projection and would like to create a single > > >> image showing the whole structure. As the intensity of the first max > > proj > > >> is higher than the second, composing both is not a good solution. > > >> > > >> I remember that there was a software that combined two images and > with a > > >> sliding rule one could vary the 'transparency of either image and get > a > > >> good solution. > > >> > > >> My question is: is there any plugin with something similar to a > > >> 'transparency sliding rule' in Fiji/ImageJ? > > >> > > >> Thank you in advance for any help. > > >> > > >> Best > > >> > > >> Antonio > > >> > > >> -- > > >> ImageJ mailing list: https://urldefense.proofpoint. > > >> com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwIBaQ&c > > >> =Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzy > > >> txHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=X2ujGcA0wkKFUzrUxOYhSPJh > > >> lxE1YBB0JMY2MnVIYd8&s=GbOuUPPLmrvK-l6iYCsXxtwBNFwTcwYJeMPd6M6RT-s&e= > > >> > > > > > > -- > > > __ > > > > > > Vytas Bindokas, Ph.D. > > > Research Assoc. Prof., > > > Director, BSD Light Microscopy Core Facility > > > phone: 773-702-4875 [alt's: 773-834-9040 or 773-834-2639] > > > > > > [address for letters ONLY (see shipping addr below):] > > > Dept Pharmacol Physiol Sci MC0926 > > > 947 E 58th Street > > > The University of Chicago > > > Chicago IL 60637 > > > Room Abbott 129 > > > > > > > > > shipping address (main KCBD site): > > > V. Bindokas > > > 900 E 57th Street > > > KCBD room 1250, Microscopy Core > > > The University of Chicago > > > Chicago IL 60637 > > > > > > > > > email [hidden email] > > > web site for LMCF: > > > http://digital.uchicago.edu > > > > > > -- > > > 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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