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  • Nov 10 22:12
    SarenT opened #139
  • Nov 09 15:13

    ctrueden on master

    Bump to next development cycle … (compare)

  • Nov 09 15:13

    ctrueden on TrackMate_-5.0.1

    [maven-release-plugin] prepare … (compare)

  • Nov 08 12:35

    tinevez on master

    Fix important TrackMate bug in … Add an error message in case so… Add the possibility to save a d… and 1 more (compare)

  • Nov 06 09:44
    hubutui commented #223
  • Nov 04 14:10
    tinevez ready_for_review #109
  • Nov 04 14:10
    tinevez edited #109
  • Nov 04 14:09
    tinevez edited #109
  • Nov 03 10:34
    tinevez edited #109
  • Nov 03 10:34
    tinevez edited #109
  • Nov 03 10:34
    tinevez edited #109
  • Nov 03 10:02
    tinevez synchronize #109
  • Nov 03 10:02

    tinevez on illuscienta-icons

    Better color scheme and sizes f… (compare)

  • Nov 02 10:19
    tinevez opened #109
  • Nov 02 10:14

    tinevez on illuscienta-icons

    Fix view JFrame icons on Window… FileChooser util - add methods … Use IlluScienta icons in the io… (compare)

  • Oct 31 08:49

    tinevez on illuscienta-icons

    Change transparency of main win… JDialog and JFrame locations ar… (compare)

  • Oct 29 13:42

    tinevez on illuscienta-icons

    Image for views depending on we… Use IlluScienta icons in views … Mediu versions of icons and Mas… and 4 more (compare)

  • Oct 28 17:05

    tinevez on illuscienta-icons

    Import icons made by IlluScient… (compare)

  • Oct 28 13:01
    tpietzsch closed #107
  • Oct 28 13:00
    tpietzsch commented #107
tpietzsch
@tpietzsch
@ctrueden Enjoy!!!
Klim Kolyvanov
@milkyklim

@milkyklim I am chatting with @kapoorlab, and he was wondering about an example of the "two-level" design of lower-level SciJava commands which work headless, repeatedly called by higher-level interactive code with a UI.

@ctrueden sorry for the late reply, was on vacation. :) This “two-level” command structury is something that is implemented in Radial Symmetry plugin. But (if you remember) there is no way to extend it properly to the ui-plugin since you can’t pass the parameters from one command to another in macro. :(

Varun Kapoor
@kapoorlab
@milkyklim Thanks, I will have a look, @tpietzsch @awalter17 I have tested the intersection of ellipses part of the code based on David Eberly code and it has been implemented in imglib2-algorithm on my branch: https://github.com/kapoorlab/imglib2-algorithm/blob/master/src/main/java/net/imglib2/algorithm/ransac/RansacModels/Intersections.java It works for getting 2D ellipse intersection points and I also have a part where you can draw tangents at the point of intersection and get the angle between them implemented. It uses quartic solvers to get the point of intersection and is working nicely, hope this is a nice addition to your Ransac based ellipsoid fits. Happy new year 2018.00 :smile:
amirffff
@amirffff
Dose somebody program with python for fiji and can help me please?
Richard Domander
@rimadoma
@ctrueden First off: hope your holiday went wellQ Second: I'm not quite clear on how to use the update sites you created for me back in Dresden. Shall I just use sites.imagej.net/pqct and sites.imagej.net/bonej with my (personal) wiki account?
Jan Eglinger
@imagejan
I think this was the idea, @rimadoma, that everybody just has their own imagej.net credentials once on their "personal" account, and Curtis adds permissions to various update sites as needed.
To avoid proliferation of "update accounts" on the wiki : )
Richard Domander
@rimadoma
@imagejan Cheers, just to clarify: that means I can't just follow to regular instructions and change the update site address?
Jan Eglinger
@imagejan
Changing an update site URL would lead to inconsistent state on Fiji installation that consume the site, no? I think this can (and should) only be done by admins and only with good arguments.
Are there instructions anywhere that explain how to change an update site URL?
Why can't you stick with the one you have, and just edit the update site name on the wiki list if necessary?
Richard Domander
@rimadoma
@imagejan Because I'm planning to maintain multiple update sites for different things. But I get your point now - i.e. the way I suggested is not the way it works
Curtis Rueden
@ctrueden
@rimadoma I'm not sure I understand the question. If you want an update site renamed, just let me know and I'll do it. If you want multiple update site URLs pointing to the same destination, I can do that too using symlinks.
And yes, for uploading, use your normal wiki account (Rdom) and upload password, set via this page—NOT the same thing as your wiki login password.
Richard Domander
@rimadoma
@ctrueden Sorry, I'll try to explain better: you remember those update sites bonej and pqct you created for me in Dresden? I'm not quite sure how to upload artefacts to them. Am I right that they're associated with my wiki account? Are their URLs sites.imagej.net/*?
Curtis Rueden
@ctrueden
Login is webdav:Rdom; pass is the one set on this page. This is distinct from your wiki password.
Instructions for uploading artifacts can be found here.
Richard Domander
@rimadoma
@ctrueden Thanks!
Curtis Rueden
@ctrueden
@HedgehogCode @frauzufall @fjug FYI, the TensorFlow update site has finally been updated today with imagej-tensorflow 0.2.0, containing the improvements done by @HedgehogCode back in September-October. Sorry for the delay on that.
Deborah Schmidt
@frauzufall
:+1:
Varun Kapoor
@kapoorlab
Hi people, I heard a talk about the RACE algorithm for segmentation, digging deep it uses viscous watershed transform: https://link.springer.com/content/pdf/10.1007/s10851-005-4893-3.pdf, is there an implementation of this algorithm in Fiji/ imagej-ops or anywhere else that you know off?
Jan Eglinger
@imagejan
@kapoorlab are you talking of this original RACE implementation: https://bitbucket.org/jstegmaier/race/overview and this paper: http://dx.doi.org/10.1016/j.devcel.2015.12.028 ?
Varun Kapoor
@kapoorlab
Thanks that helps, I also wanted to know if there is an implementation of viscous watershed transform.
ksebas3
@ksebas3
How do I know the wavelength of the image if I am using 2-photon confocal micoscopy? I have up to 2 to 3 channels but I can't tell from the metadata what wavelengths are being used? Can someone explain? Thank you!
Curtis Rueden
@ctrueden
@kapoorlab Did you try to connect to an ImageJ update site unsuccessfully recently? It seems someone in Szeged got their IP banned over the weekend trying to log in as vkapoor. ;-)
If you did not manage to get it working, try with capital V.
Varun Kapoor
@kapoorlab
Oh, ha and yeah that was me trying to fix the jfreechart thing that you fixed a while ago but I only got myself to merge that with my branch now and then I did get that working over the weekend 😊 and thanks for the fix as well. Hi from segzed, it's a perfect ghost town in the evenings! I guess that the IP is unbanned now though right?
Curtis Rueden
@ctrueden
@kapoorlab It should not be permanently banned. Let me know if you continue having trouble.
Varun Kapoor
@kapoorlab
@ctrueden yeah it works, just checked. thanks.
jfcollard
@jfcollard
Hello all. I'm an absolute beginner with ImageJ/Fiji. I've been able to apply a few useful built-in tools to my CT scans, but many of the filters fail because my images have a background. The kind of images I look at can be found here: https://blog.highmarkhealth.org/low-dose-ct-scans-show-promise-in-detecting-early-stage-lung-cancer/lungcancer/ As you can see, anything outside the inscribed circle is useless background. My question to the community is: How do you suggest I get rid of this background? Can I do this using the existing functions, or do I have to write my own script or plug-in? (additional detail that may be of help: for my purposes, it would be OK to merge the background with the dark, textured parts at the top and bottom of the disk.) Thanks in advance!!
Ellen T Arena
@etarena
Hey @jfcollard - this is a great question for the ImageJ Forum - would you mind posting it there??
Curtis Rueden
@ctrueden
@jfcollard The basic idea would be to generate a circular ROI covering the area of interest, and nothing else, and then do your filtering on that. If you can avoid drawing the circle by hand, it is much better/faster/reproducible. But for detailed discussion of how to proceed I agree with @etarena that the forum is the best place.
amirffff
@amirffff
does someone work with imagej and python?
I have smoe questions
Kyle I S Harrington
@kephale
@amirffff try http://forum.imagej.net/ and you will definitely catch the attention of imagej + python folks
amirffff
@amirffff
thanx
jfcollard
@jfcollard
@etarena Thanks Ellen! Doing now
jfcollard
@jfcollard
@ctrueden Thanks Curtis. One concern I have is that the ROI may be slightly different for each CT scan, or even for each slide of the 3D scan. Can a ROI be determined automatically, possibly based on the fact this background lies in corners and is always pitch black? Any advice greatly appreciated. -JF
amirffff
@amirffff
HI
@amirffff
HI
deos someone know if there is way to write a script for imagej with python?
Ulrik Günther
@skalarproduktraum
@amirffff have a look at http://imagej.net/Jython_Scripting
@ctrueden is there already some kind of timeline to switch fiji to java9? (i hope i’m not poking any wounds here :D )
Curtis Rueden
@ctrueden
@skalarproduktraum Why do you need Java 9?
Ulrik Günther
@skalarproduktraum
@ctrueden just gauging at the moment, but java 9 introduces Math.fma() e.g., which is very useful for me
Curtis Rueden
@ctrueden
We recently fixed the ImageJ launcher so that you can at least start ImageJ with Java 9 successfully. Planning to iron that out more this year. But no plans yet for when to start requiring Java 9 (or 10) for core libs.
If Scenery/SciView continues to ship on its own update site then it certainly would be possible for it to start requiring Java 9 soon.
Ulrik Günther
@skalarproduktraum
okay, thanks, i’ll try to investigate a bit deeper whether we gain enough from the improvements so warrant requiring java 9
KaraokeMary
@KaraokeMary
Hello, I just need some very basic help with a three plane CT scan and getting the coordinates to normalize.
I can't seem to make the XYZ global among all three planes. There must be a way to do this, right?