Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
  • 16:19
    maarzt commented #187
  • 15:04
    maarzt synchronize #188
  • 15:04

    maarzt on fix-trackscheme-merging-spots

    Fix LineageTreeLayout to work f… (compare)

  • 14:42
    maarzt opened #188
  • 14:42
    maarzt review_requested #188
  • 14:37

    maarzt on fix-trackscheme-merging-spots

    Fix LineageTreeLayout to work f… (compare)

  • 14:21

    maarzt on fix-trackscheme-merging-spots

    Fix LineageTreeLayout to work f… (compare)

  • 07:56
    tinevez commented #187
  • Aug 10 09:18
    maarzt commented #187
  • Aug 10 09:17
    maarzt assigned #187
  • Aug 10 07:51
    maarzt opened #187
  • Aug 02 13:47
    maarzt review_requested #186
  • Aug 02 13:46
    maarzt synchronize #186
  • Aug 02 13:46

    maarzt on edit-branch-label

    Add BranchTrackSchemEditLabelAc… (compare)

  • Aug 02 13:45
    maarzt edited #186
  • Aug 02 13:44
    maarzt edited #186
  • Aug 02 13:43
    maarzt opened #186
  • Aug 02 13:25

    maarzt on edit-branch-label

    LineageTreeLayout: add class De… LineageTreeLayout: remove unuse… Refactor LineageTreeLayout: ext… and 23 more (compare)

  • Jul 29 06:51
    tinevez commented #181
  • Jul 29 06:48
    tinevez closed #182
areya984203
@areya984203
Hello, I have been trying to download fiji on my macbook but keep getting the message above ^ Any help would be greatly appreciated!
odinsbane
@odinsbane
Is it an M1 mac?
12 replies
Shambhavi Aggarwal
@agg-shambhavi
How to do an undo in labkit?
2 replies
Christian Tischer
@tischi

../scijava-scripts/release-version.sh

Newer version of parent 'org.scijava:pom-scijava' is available: .
I recommend you update it before releasing.

@imagejan @ctrueden could it tell you which is the new version?

2 replies
Christian Tischer
@tischi
@ctrueden in the parent-pom 32.0.0-beta-4 there is jdhf5 version 19.04.0 and bdv-core version 10.2.2, which still uses the old jhdf5. Did you maybe overlook this?
2 replies
I had a look and it seems we would need bdv-core 10.3.1 to be compatible with the new jdh5.
Christian Tischer
@tischi
Hm, the current Fiji still ships jdh5 version 14.12.6.
Ah, I see, the current Fiji is in fact version 2.3.0, which still uses the scijava parent pom 31.0.0, right?
Christian Tischer
@tischi
I changed now some of my code to work with the new jdh5...
Should I roll this back if I want to ship things with the current Fiji? Or could I ship the new jdhf5 library with my update site (this would probably break a lot of things, would it)?
Christian Tischer
@tischi
@NicoKiaru which version of bdv-playground to you currently ship and which parent pom does that use?
Nicolas Chiaruttini
@NicoKiaru
Hi @tischi I kept 31.1.0, I saw beta in 32.0.0-beta-4 so I'm not using it right now
Christian Tischer
@tischi
OK @NicoKiaru, I will do the same then. And which version of bdv-playground do you currently ship?
Nicolas Chiaruttini
@NicoKiaru

This one:

<dependency>
  <groupId>sc.fiji</groupId>
  <artifactId>bigdataviewer-playground</artifactId>
  <version>0.4.5</version>
</dependency>

there hasn't been a lot of changes for a while, which is good I think

Curtis Rueden
@ctrueden
Yes, I advise against using the beta POM unless you really need it now.
It is not well tested yet, which is why it is beta. There are known discrepancies. It's also why I did not update Fiji to those component versions.
You can of course start updating your projects to use the newer JHDF5 and so forth, so that you are ready when a new non-beta POM does drop. But @hinerm and I are still working on it. We will send out a clear communication after pom-scijava 32.0.0 is released, so that people have time to respond and update, before we push out the changes to the core update sites. Unfortunately, I got COVID from the CZI trip, so I will be slow(er than usual) for a while pushing on this.
@tischi @NicoKiaru In the meantime, if y'all can file issues on scijava/pom-scijava documenting the specific discrepancies, and put them into the next-release milestone, that would be extremely helpful.
Christian Tischer
@tischi
2 replies
Christian Tischer
@tischi
when depending on the parent pom, I somehow remember that one should not put this?! Could someone remind me why that is?
    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>2.19</version>
                <configuration>
                    <argLine>-Xmx1024m</argLine>
                </configuration>
            </plugin>
        </plugins>
    </build>
I am asking because I may have to allocate more RAM for running tests in the CI...
Christian Tischer
@tischi
I found out. If one does not specify this, it will automatically download the mvn plugin.
Curtis Rueden
@ctrueden
@tischi I'd like to make it easier to up the RAM without adding that block. We use properties whenever possible. Let's take a look at pom-scijava-base...
You could try setting scijava.surefire.args but I don't know what happens if you pass two different -Xmx values in a row (which is what would happen if you did that). Worth a try.
If it doesn't work, we can add a new property for surefire memory allocation specifically.
I would caution that if you need more than 512MB to run unit tests, they aren't really "unit tests" anymore. But I understand there are edge cases where you might need it. Still, ask yourself if you really need it. :smile:
N-itin
@N-itin
Can Anyone tell, How can i read a CSV file which have x,y and intensity data? So that i can have an image from that csv file?
I have tried the import option but it only opens the table and does not show the image.
Curtis Rueden
@ctrueden
@N-itin The Image → Transform → Results to Image command can convert a table to an image. It might depend on how your table ends up structured, though. For more help, please post at https://forum.image.sc/ with tag fiji!
Minli-hub
@Minli-hub
Hi everyone, I am using WEKA segmentation. The out-of-bag error increases by 4.7% as I add more voxels (Sample: 18001794151 Voxels. Total labeled voxels: 234 174. Pore voxels: 121 900, Not pore voxels: 112 274). How can I decrease the out-of-bag error? Many thanks!
MichaelSNelson
@MichaelSNelson
Hi @Minli-hub, as described in the comment directly above, that question is more about image analysis than programming, and would be a better fit to the image.sc forum. You may want to include the weka tag as well.
Minli-hub
@Minli-hub
OK. Many Thanks!
Jean-Yves Tinevez
@tinevez
I would need your opinion about video encoding from Fiji.
In the Fiji.app repo we ship ffmpeg. But is there a java binding, shipped with Fiji I could use in a Fiji plugin?
I also consider using https://github.com/artclarke/humble-video
It has a maven artifact I could play with, but the jars amount to 100M.
Could I ship with my plugin (its mastodon, it's been mastodon all along)?
Curtis Rueden
@ctrueden
@tinevez The only thing right now is the FFMPEG update site that Johannes made, but it is not maintained.
Jean-Yves Tinevez
@tinevez
Thank you!
I went for humble as a demo for now. I could use it to capture an animation in a BDV window and export it to a MP4 directly:
Jean-Yves Tinevez
@tinevez
New things are coming to the next TrackMate. Among them:
I still need to fix javadoc errors, but I should be able to release this week-end,
along with a few novelties on the TrackMate-Helper side.
Gabriel Selzer
@gselzer
:heart:
Curtis Rueden
@ctrueden
Heads up: I have created a #Fiji channel on the image.sc Zulip.
odinsbane
@odinsbane
Will the Zulip replace the Gitter?
1 reply
Mark Hiner
@hinerm
@axtimwalde did something change?
7 replies