ImageJ wiki is read-only

You can download Kappa-1.7.3.jar-20191204171846 directly from the update site repository, rename the file to Kappa-1.7.3.jar and put it into your ./Fiji.app/jars/ folder.

That should be sufficient, unless there are some missing dependencies that you also require, I’m not sure about this. @hadim can possibly clarify.

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That worked! Thanks!

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New user here.
I came across this site for my colleague and I is trying to conduct a research on retinal vasculatures. I know that many sources suggested to use Vessel Analysis. But, now that the imagej.net is down, I am in no way of downloading it. And I cannot find any files in repository or the update sites.
Anyone can help with such file, as to where to download it?

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Hey @razzrafa,

thanks to @schmiedc hint:

You can read it here:

Let us know if this works!

Cheers,
Robert

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I made a lot of progress today:

  • LOCI’s internal equipment reservation calendar system is up and running now on the new infrastructure. This is relevant because it requires a similar PHP infrastructure to imagej.net, so we’ve taken several necessary foundational steps toward restoring the wiki.

  • Migrated five more sites to the new infrastructure.

  • Did some heavy cleaning & updates to our subnet’s firewall rules, internal knowledge base and issue tracker. This is important for future maintainability.

  • Solved issues relating to SSL certificate chains (did you know the 20-year-old AddTrust root certificate expired this past May 30? And any existing certs you have referencing it won’t work with old client software? Fun times!)

Current status: 22 of 38 sites migrated!

Tomorrow I’m going to prioritize the minimal imagej.net rules to make the Updater work again, hopefully squashing the infinite redirect loops people have reported in the process.

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Dear Curtis,

Thank you so much for all the work that is usually hidden in maintaining this flourishing community and software ecosystem.
Is there something the community can do to help things in the long run? Like setting up mirrors in different University servers to alleviate loads of some websites? Any better ideas or suggestions welcome.

Thank you again for all this incredible commitment

Sincerely,
Oli

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Today’s updates:

  • The ImageJ Updater is working again! :tada:
  • The ImageJ wiki has a maintenance page configured now, with links to cached content and other resources.
  • The missing OpenSPIM downloads are now available again.
  • 3 more sites migrated, 13 to go: 25/38=65%

@Preetika Glad you were able to install Kappa using the workaround. For future reference, the normal update mechanism (Help › Update…, “Manage Update Sites” button, tick the sites you want) should now be working again. Let us know here if not.

@eljonco @mmvpgs I finally got a maintenance page up. It has links to cached versions of imagej.net from the Wayback Machine as well as Google’s cache (the Wayback Machine’s version is much easier on the eyes :wink:). With this, the infinite redirects problem should be fixed—let us know here if not (though try clearing your browser cache first too).

@17adaell Thank you for pointing this out! I have restored the contents of openspim.org/downloads to https://downloads.imagej.net/openspim/; I hope this is helpful. Let us know here if you notice any other missing resources.

@oburri Definitely, thanks for asking. We’ve been running an rsync daemon so that people can mirror update.imagej.net, update.fiji.sc and sites.imagej.net. We’ll be publicizing that more widely in future, and maybe we can have a mirrors list that the Updater can use, or even set up a CDN. All these things take additional time and development resources but it will be good to have the redundancy, and could really help with performance for different geographic areas. As for the wiki, we are currently far along in the process of ditching MediaWiki (:joy: but also :cry:) in favor of GitHub Pages, which will have many advantages, and avoid this sort of problem in the future. We can discuss more along these lines in the coming weeks, once the server situation is further along.

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Fantastic news @ctrueden! Thank you and the team so much for the hard work (even on holidays apparently)!

Sounds like a fantastic idea! I’m a big fan of redundancy for fail-safe systems. Happy to setup another mirror and ease their use. Afaik at the moment, ImageJ doesn’t read update sites from mirrors. If you need developer support or testers for this let me know!

Thanks again for taking care of all this :blue_heart::green_heart::heart:

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Thanks for the suggestion on the cached view. I have already done that and currently, we are calculating using the formula. Yet, we still need a workaround on how to automatize vessel diameter measurement since there is a lot of work to do. I came across a source code on GitHub on this plugin but could not get the macros to work. Hopefully the site is on very soon.

Very big thanks for all the effort you and your team puts in all the infrastructure and maintenance. That is worth so much and realized as well as appreciated so little. Even I just realized how much I sometimes depend on the updater etc. Potentially, this shutdown helps that the whole user community also understands that functioning software should not be taken simply for granted.
I don’t have the experience in helping with any development in that direction but I am happy to support any testing phase.

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@razzrafa Ah, from your first post I did not understand that Vessel Analysis is not available from a proper ImageJ update site. That is unfortunate. I have now grabbed the Vessel_Analysis.zip file and attached it here for you. Hope that helps.

Vessel_Analysis.zip (3.4 KB)

You’ll also need to install the Mexican Hat Filter plugin, available from here.

I don’t know whether the plugin authors frequent this forum; but if you have issues or questions you can post a new topic here on the forum and a moderator can use the Invite feature to invite them to respond to you.

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Today’s update: 4 more sites migrated; 9 still to go. 29/38=76%. I also improved some of the regression tests. (Yeah, regression tests! :joy: They were long overdue. They make it much easier to verify whether intended functionality keeps working as the configuration evolves.)

Tomorrow, several ImageJ team members will be meeting to plan completion of the ongoing migration of the ImageJ wiki from MediaWiki to GitHub Pages. Here is a bonus for reading this far: a sneak peek at the new imagej.net design. Keep in mind it’s not the entire site contents yet—just a selection of pages proving viability of the new design. Our next major step is to migrate the entire existing wiki en masse, then ask for the community’s help in reviewing and fixing any lingering formatting errors.

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@ctrueden Thank you for the help

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Actually, I cannot confirm this, unfortunately :confused:

On Windows 10, with a Fiji installation using a proxy behind a firewall, I still get the following error message (no matter if trying with ij-1.52p.jar [the one from an up-to-date Fiji] or with ij-1.53c.jar [the one that respects the proxy setting for HTTPS connections]):

[ERROR] Cannot connect to the Internet.
Do you have a network connection?
Are your proxy settings correct?
[ERROR] java.io.IOException: Unexpected response code: 200
	at net.imagej.ui.swing.updater.ImageJUpdater.testNetworkConnection(ImageJUpdater.java:373)
	at net.imagej.ui.swing.updater.ImageJUpdater.errorIfNetworkInaccessible(ImageJUpdater.java:324)
	at net.imagej.ui.swing.updater.ImageJUpdater.run(ImageJUpdater.java:101)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

Hello,

I have been using the archive folder on the downloads page to download a specific version of the Fiji jars. I noticed today that that link is no longer working, and I found this thread. I see that there are several versions available for download in the archive folder, just not the one I use (20200225-2146). Is this related to the migration? Or, is it gone for good?

Thanks for your help!

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Hi @elleneme234,

they got deleted because the build process only partially uploaded them (this issue is now resolved and unrelated to the current server outage). You can still download them from our MPI-CBG downloads mirror. If they are valuable, we can also restore them on the official downloads server.

Best,
Deborah

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Yes, please! They are valuable and will become more valuable in the future :wink:

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Hi @frauzufall,

Thank you for the response! I am using the Fiji jars within an automated pipeline built with docker, so I would like to download a set version of the jars both for reproducibility and to avoid breaking changes to my code and build process. The best approach I found on my own was to grab the jars from the archive page, but if there is a more robust/recommended approach, I’d be happy to try that.

Thanks!

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Hi, does anybody have the TrackMate manual as pdf? I didn’t download it and was only accessing it through the website :frowning:

This one? TrackMate-manual.pdf (12.9 MB)

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