Hi Toby,<br><br><blockquote style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;" class="gmail_quote"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Probably I should send this to the mailing list</span><br>
</blockquote><br>Sure, I am CCing the list.<br><br><blockquote style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;" class="gmail_quote"><span style="font-size: 11pt; color: rgb(31, 73, 125);">It looks like they put the wrong classname in the bat file.</span><br>
<span style="font-size: 11pt; color: rgb(31, 73, 125);"></span></blockquote><span style="font-size: 11pt; color: rgb(31, 73, 125);"><br></span>Thanks for letting me know. The problem was that we were accidentally linking to an obsolete location of the application build (and hence an older version). I have updated the downloads page to point to the latest code now, so the ZIP file should work again out of the box.<br>
<br><blockquote style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;" class="gmail_quote"><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">I was able to open
the blobs file and do thresholding, but I was unable to open up a jpeg
file. <br></span></p></blockquote><span style="font-size: 11pt; color: rgb(31, 73, 125);"></span><br>Right now, File > Open does not handle color images properly. If you do File > Import > Bio-Formats you will be able to import the color images as grayscale with a slider for channel. Note that any menu icon with the ImageJ microscope item (e.g., File > Open) is an ImageJ 1.x plugin being run in compatibility mode, while menu icons without it are IJ2 plugins (e.g., File > Import > Bio-Formats).<br>
<br>We will try to have the color image problem addressed by the April 1st release of 2.0alpha1.<br><br>Regards,<br>Curtis<br><br><div class="gmail_quote">On Fri, Mar 11, 2011 at 12:03 PM, Toby Cornish <span dir="ltr"><<a href="mailto:tcornis3@jhmi.edu">tcornis3@jhmi.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div link="blue" vlink="purple" lang="EN-US"><div><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Curtis, </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">We are very excited about developments on the imagejdev. Probably I should send this to the mailing list, but the bat file that comes with the pre-alpha doesn’t seem to work without modification (see below)</span></p>
<p class="MsoNormal"><a name="12ea6162ff95ca5e__MailEndCompose"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></a></p><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Toby</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p><div><div style="border-width: 1pt medium medium; border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; padding: 3pt 0in 0in;">
<p class="MsoNormal"><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;"> James Morgan [mailto:<a href="mailto:jmorgan@jhmi.edu" target="_blank">jmorgan@jhmi.edu</a>] <br><b>Sent:</b> Friday, March 11, 2011 12:30 PM<br>
<b>To:</b> Toby Cornish; <a href="mailto:demarzo.angelo@gmail.com" target="_blank">demarzo.angelo@gmail.com</a><br><b>Cc:</b> 'Bora Gurel'; Angelo Demarzo<br><b>Subject:</b> RE: Next generation imageJ</span></p></div>
</div><p class="MsoNormal"> </p><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Toby,</span></p><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"><br>It looks like they put the wrong classname in the bat file. Change the text in image.bat to say:<br>
@echo off java -mx512m -cp "jar\*" imagej.gui.swing.MainFrame $@</span></p><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">This will allow you to at least start the application. I was able to open the blobs file and do thresholding, but I was unable to open up a jpeg file. This is even after I updated my jar files to get the latest daily build. But they are a pre-alpha version. This development looks really promising.</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Jim</span></p><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p><div><div style="border-width: 1pt medium medium; border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; padding: 3pt 0in 0in;">
<p class="MsoNormal"><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;"> Toby Cornish [mailto:<a href="mailto:tcornis3@jhmi.edu" target="_blank">tcornis3@jhmi.edu</a>] <br><b>Sent:</b> Friday, March 11, 2011 12:08 PM<br>
<b>To:</b> '<a href="mailto:demarzo.angelo@gmail.com" target="_blank">demarzo.angelo@gmail.com</a>'<br><b>Cc:</b> James Morgan; Bora Gurel; Angelo Demarzo<br><b>Subject:</b> RE: Next generation imageJ</span></p></div>
</div><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">I tried installing and running their pre-alpha, but I got this error. Jim, any thoughts on this error?</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">C:\Users\tcornis3\bin\imagejdev>imagej.bat</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Exception in thread "main" java.lang.NoClassDefFoundError: imagej/gui/MainFrame</span></p><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Caused by: java.lang.ClassNotFoundException: imagej.gui.MainFrame</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> at java.net.URLClassLoader$1.run(Unknown Source)</span></p><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> at java.security.AccessController.doPrivileged(Native Method)</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> at java.net.URLClassLoader.findClass(Unknown Source)</span></p><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> at java.lang.ClassLoader.loadClass(Unknown Source)</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)</span></p><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> at java.lang.ClassLoader.loadClass(Unknown Source)</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Could not find the main class: imagej.gui.MainFrame. Program will exit.</span></p><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Toby</span></p><p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p><div style="border-width: 1pt medium medium; border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; padding: 3pt 0in 0in;">
<p class="MsoNormal"><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;"> Angelo De Marzo [mailto:<a href="mailto:demarzo.angelo@gmail.com" target="_blank">demarzo.angelo@gmail.com</a>] <br><b>Sent:</b> Friday, March 11, 2011 12:00 PM<br>
<b>To:</b> Toby Cornish<br><b>Cc:</b> James Morgan; Bora Gurel; Angelo Demarzo<br><b>Subject:</b> Re: Next generation imageJ</span></p></div><p class="MsoNormal"> </p><p class="MsoNormal" style="margin-bottom: 12pt;">very cool indeed! thanks</p>
<div><p class="MsoNormal">On Thu, Mar 10, 2011 at 3:30 PM, Toby Cornish <<a href="mailto:tcornis3@jhmi.edu" target="_blank">tcornis3@jhmi.edu</a>> wrote:</p><div><div><p class="MsoNormal">Looks very promising</p><p class="MsoNormal">
</p><p class="MsoNormal"><a href="http://imagejdev.org/" target="_blank">http://imagejdev.org/</a></p><p class="MsoNormal"> </p><p class="MsoNormal">Toby C. Cornish, M.D., Ph.D.</p><p class="MsoNormal">Gastrointestinal and Liver Pathology</p>
<p class="MsoNormal"> </p><p class="MsoNormal">Johns Hopkins University</p><p class="MsoNormal">Department of Pathology</p><p class="MsoNormal">401 N. Broadway</p><p class="MsoNormal">Weinberg Rm. 2242</p><p class="MsoNormal">
Baltimore, MD 21231</p><p class="MsoNormal"> </p><p class="MsoNormal"><a href="tel:410-955-3580" target="_blank"></a><a href="tel:410-955-3580" target="_blank">410-955-3580</a> Phone</p><p class="MsoNormal"><a href="tel:410-955-0115" target="_blank"></a><a href="tel:410-955-0115" target="_blank">410-955-0115</a> Fax</p>
<p class="MsoNormal"><a href="tel:410-434-2824" target="_blank"></a><a href="tel:410-434-2824" target="_blank">410-434-2824</a> Pager</p><p class="MsoNormal"> </p></div></div></div><p class="MsoNormal"> </p></div></div></blockquote>
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