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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?
Curtis Rueden
@ctrueden
@KaraokeMary Could you describe what you mean by "XYZ global among all three planes"? Isn't each plane its own Z plane?
Curtis Rueden
@ctrueden
@KaraokeMary I see you also posted to the ImageJ mailing list. That is a better place to solve your issue than here in Gitter. (Although best would be http://forum.imagej.net/ rather than the mailing list.)
KaraokeMary
@KaraokeMary
I did, but so far no luck. The XYZ coordinates in the selection tools is different depending on if I am in sagittal, coronal, or transverse. The X is always on the left and the Y is always at the top, regardless of plane. I need them to make them correspond somehow though all three.
KaraokeMary
@KaraokeMary
I posted on the forum a few days ago, but no luck.
Ellen T Arena
@etarena
@KaraokeMary - I saw your post on the forum... Perhaps it's worth adding a bit more detail in your post? Change the title to be more specific for what you need? Which tools specifically are you using? Write out your current workflow and where you find it's 'breaking' down... if you can include an original dataset - that is also super helpful for us all to help you. :)
@KaraokeMary - I just updated the title of your post on the Forum... feel free to edit it again. Let's see if we can get you the help you need.
Varun Kapoor
@kapoorlab
Hi did somebody notice that if I do this : https://imagej.net/File:MavenRunConfig.png for a maven based Java project and try to open Fiji it quits during opening always?
Curtis Rueden
@ctrueden
@kapoorlab Nope, I don't use Eclipse that way. If you have time to troubleshoot and report back more details (or better: find a fix and update the wiki to reflect that fix), it would be much appreciated.
irsasho
@IrsaShoukat_twitter
Hello everyone. I am new to image j and need some guidance. I have a time lapse where each time point has multiple stacks (7 per time point). Is there a plug in that will automatically detect the best stack for me (instead of me having to do this manually) ?
Ellen T Arena
@etarena
@IrsaShoukat_twitter - the best place to post this type of question is on the ImageJ Forum ... it's easier to get more detailed, searchable feedback there. :) Just include as much detail (and example image?) as you can... we'll get you help!
irsasho
@IrsaShoukat_twitter
ok! thank you :)
Ellen T Arena
@etarena
:)