Cannot see plugins in my ImajeJ plugin folder on Mac
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Hi,
I downloaded ImageJ for Mac and downloaded Loci and Bio-formats files (and unzipped) into ImageJ plugins folder according to instructions given on Open Microscopy (http://www.openmicroscopy.org). However, I cannot open my files and cannot see these plugins in ImageJ scroll-down plugin menu. I would be grateful if someone could help. I really need this for analysis of my data. Thank you |
Re: Cannot see plugins in my ImajeJ plugin folder on Mac
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Hi Saman,
> I downloaded ImageJ for Mac and downloaded Loci and Bio-formats files (and > unzipped) into ImageJ plugins folder according to instructions given on Open > Microscopy (http://www.openmicroscopy.org). However, I cannot open my files > and cannot see these plugins in ImageJ scroll-down plugin menu. I would be > grateful if someone could help. I really need this for analysis of my data. You should not need to unzip the bioformats_package.jar file; just moving it to your ImageJ plugins folder is sufficient. If the file is named bioformats_package.zip when you download it, then it will need to be renamed to bioformats_package.jar after being moved. Regards, -Melissa On Fri, Aug 08, 2014 at 12:36:26AM -0700, Saman wrote: > Hi, > > I downloaded ImageJ for Mac and downloaded Loci and Bio-formats files (and > unzipped) into ImageJ plugins folder according to instructions given on Open > Microscopy (http://www.openmicroscopy.org). However, I cannot open my files > and cannot see these plugins in ImageJ scroll-down plugin menu. I would be > grateful if someone could help. I really need this for analysis of my data. > > Thank you > > > > -- > View this message in context: http://imagej.1557.x6.nabble.com/Cannot-see-plugins-in-my-ImajeJ-plugin-folder-on-Mac-tp5009068.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 |
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Hi Melissa, Thanks a lot. The name of the file in my ImageJ plugins folder is correct and I didn`t need to change it or unzip it. However, when I open ImageJ which I have very recently installed, I cannot see anything at all in the Plugins pull-down menu. I also cannot open microscopy files by drag and dropping them onto ImageJ. I never had this type of problem when I was using windows. I wonder if this is a Mac problem.
On Fri, Aug 8, 2014 at 11:34 PM, Melissa Linkert-2 [via ImageJ] <[hidden email]> wrote:
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Hi Saman,
> when I open ImageJ which I have very recently installed, > I cannot see anything at all in the Plugins pull-down menu. I tried downloading ImageJ 1.48 from http://imagej.net/download.html and could not reproduce this problem. It is almost certainly some sort of installation issue. Did you try Fiji? It is a distribution of ImageJ that comes with Bio-Formats and other useful plugins pre-installed. It is based on ImageJ2, which includes an Updater component that makes managing plugins much easier. http://fiji.sc/Downloads Regards, Curtis On Sun, Aug 10, 2014 at 4:03 AM, Saman <[hidden email]> wrote: > Hi Melissa, > > Thanks a lot. The name of the file in my ImageJ plugins folder is correct > and I didn`t need to change it or unzip it. However, when I open ImageJ > which I have very recently installed, I cannot see anything at all in the > Plugins pull-down menu. I also cannot open microscopy files by drag and > dropping them onto ImageJ. I never had this type of problem when I was > using windows. I wonder if this is a Mac problem. > > > > > On Fri, Aug 8, 2014 at 11:34 PM, Melissa Linkert-2 [via ImageJ] < > [hidden email]> wrote: > > > Hi Saman, > > > > > I downloaded ImageJ for Mac and downloaded Loci and Bio-formats files > > (and > > > unzipped) into ImageJ plugins folder according to instructions given on > > Open > > > Microscopy (http://www.openmicroscopy.org). However, I cannot open my > > files > > > and cannot see these plugins in ImageJ scroll-down plugin menu. I would > > be > > > grateful if someone could help. I really need this for analysis of my > > data. > > > > You should not need to unzip the bioformats_package.jar file; just moving > > it > > to your ImageJ plugins folder is sufficient. If the file is named > > bioformats_package.zip when you download it, then it will need to be > > renamed to bioformats_package.jar after being moved. > > > > Regards, > > -Melissa > > > > On Fri, Aug 08, 2014 at 12:36:26AM -0700, Saman wrote: > > > > > Hi, > > > > > > I downloaded ImageJ for Mac and downloaded Loci and Bio-formats files > > (and > > > unzipped) into ImageJ plugins folder according to instructions given on > > Open > > > Microscopy (http://www.openmicroscopy.org). However, I cannot open my > > files > > > and cannot see these plugins in ImageJ scroll-down plugin menu. I would > > be > > > grateful if someone could help. I really need this for analysis of my > > data. > > > > > > Thank you > > > > > > > > > > > > -- > > > View this message in context: > > > http://imagej.1557.x6.nabble.com/Cannot-see-plugins-in-my-ImajeJ-plugin-folder-on-Mac-tp5009068.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 > > > > > > ------------------------------ > > If you reply to this email, your message will be added to the discussion > > below: > > > > > http://imagej.1557.x6.nabble.com/Cannot-see-plugins-in-my-ImajeJ-plugin-folder-on-Mac-tp5009068p5009071.html > > To unsubscribe from Cannot see plugins in my ImajeJ plugin folder on > Mac, click > > here > > < > > > > . > > NAML > > < > http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml > > > > > > > > > -- > View this message in context: > http://imagej.1557.x6.nabble.com/Cannot-see-plugins-in-my-ImajeJ-plugin-folder-on-Mac-tp5009068p5009080.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 |
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Hi Curtis, Thanks a lot. You are right, it did seem like an installation issue. I can use ImageJ and install plug-ins easily now after reinstallation. I am also looking into Fiji. We have it on another computer in our lab and it seems to be easy to use.
On Sat, Aug 23, 2014 at 4:07 AM, Curtis Rueden [via ImageJ] <[hidden email]> wrote: Hi Saman, |
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In reply to this post by ctrueden
Hi Curtis, I just installed Fiji. It`s amazing! It has everything I need and it is very easy to use. The timing could`t haven been better as I have a lot data to analyse. Thanks everyone for guiding me through this, Saman On Mon, Aug 25, 2014 at 2:39 PM, Saman Ebrahimi <[hidden email]> wrote:
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