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Fiji fiji https://fiji.sc/ A "batteries included" distribution of ImageJ for scientific image analysis

fiji/AnalyzeSkeleton 16

ImageJ/Fiji plugin to analyze 2D and 3D skeleton images

fiji/bUnwarpJ 16

ImageJ/Fiji plugin for consistent elastic registration of 2D images

fiji/Colocalisation_Analysis 15

Fiji's plugin for colocalization analysis

fiji/cookbook 15

Plugins collated for the Fiji Cookbook

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issue closedfiji/fiji

How can I save 16 bit images sequence to amira ascii format

How can I save 16 bit images sequence to amira ascii format. Works when images are 8 bits.

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gitlabspy

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Mark Hiner

commit sha c6647c9fdd04a548cab7cd60846a8d7bf3fa620f

Bump to pom-scijava 30.0.0 This is not strictly necessary, but pom-scijava 12.0.0 + pom-scijava-base 2.0.0 do not have a version property for net.imagej:ij, instead using the older imagej1.version, which can make attempts at overriding the version unexpected.

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Fiji library to perform image segmentation based on the Weka learning schemes

https://imagej.net/Trainable_Weka_Segmentation

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Jean-Yves TINEVEZ

commit sha 93df81052d3e1a3c8b6cd45bbaa50f3190158253

A utility that returns an iterable over a spot in an ImgPlus. Takes into account whether the spot has a ROI or not, and borderline cases.

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Jean-Yves TINEVEZ

commit sha e58971fec52104635831dc00545e3e0a6eba5172

Don't sample SpotRoi over singleton dimension.

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Jean-Yves TINEVEZ

commit sha e2bcf0a70125cae3cbf0d95a36c09ae485bcf204

Fix the label exporter action. - It was not taking into account the calibration. - Now it sample ROIs if the spot has one.

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Jean-Yves TINEVEZ

commit sha 41262ae85007c1923142f88b5f6466084c4fe6bd

Utility to reslice an ImgPlus at frame and channel. Used repeatingly in TrackMate, but calling deprecated methods.

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Jean-Yves TINEVEZ

commit sha d317ce5d6f3bdb292ff52d2430e9e3179595bcf1

Don't rely on removed TMUtils method to find z-axis.

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Jean-Yves TINEVEZ

commit sha 12a01fe073f49badb11d06cbd729b5d0d5c6c7b6

Remove deprecation warnings due to the use of HyperSliceImgPlus.

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Jean-Yves TINEVEZ

commit sha 95fd4dee0ee480176ad6431866f4c2a0486ee88f

Use the util to get a spot iterable in the spot intensity analyzer.

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Jean-Yves TINEVEZ

commit sha a3659d8980e293dc0be19e8e67ba4e241f29e989

Don't use methods removed in TMUtils to find an axis.

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Jean-Yves TINEVEZ

commit sha 4e1dad5b069b0164dfcb86eb785c43f7259077cc

Update AbstractSemiAutoTracker so that it does not rely on deprecated code.

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Jean-Yves TINEVEZ

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Update the LAP frame-to-frame linker so that it does not use deprecated code.

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Jean-Yves TINEVEZ

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Code style changes.

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Jean-Yves TINEVEZ

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Rework NN tracker so that it does not use deprecated code.

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tagfiji-2.2.0

A "batteries-included" distribution of ImageJ :battery:

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Mark Hiner

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Bump to next development cycle Signed-off-by: Mark Hiner <hinerm@gmail.com>

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Mark Hiner

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Bye bye 2020!

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Mark Hiner

commit sha 3a9a9f464a626b7c2db4025c333511ecec8680f2

Bump to pom-scijava 30.0.0 * Updates SNT components. See https://github.com/scijava/pom-scijava/pull/155 * Removes Kappa/FilamentDetector version pins

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A "batteries-included" distribution of ImageJ :battery:

https://fiji.sc/

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Jean-Yves TINEVEZ

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Let the manual detector enable morphological spot analyzers.

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issue commentfiji/fiji

How can I save 16 bit images sequence to amira ascii format

or just save as ascii instead or binary?

gitlabspy

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Pull request review commentfiji/fiji

Add standard deviation projection method

 macro "Time-Lapse Color Coder" {  function showDialog() { 	lutA = getList("LUTs");+	projection = newArray("Max Intensity","Standard Deviation"); //new array for maximum projection methods  	Dialog.create("Color Code Settings"); 	Dialog.addChoice("LUT", lutA); 	Dialog.addNumber("start frame", Gstartf); 	Dialog.addNumber("end frame", Gendf);+	Dialog.addChoice("Maximum Projection", projection);

All of these are good points. I've made those changes. Thanks for the suggestion.

pr4deepr

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PullRequestReviewEvent

startedfiji/TrackMate

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issue openedfiji/fiji

How can I save 16 bit images sequence to amira ascii format

How can I save 16 bit images sequence to amira ascii format. Works when images are 8 bits.

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Jean-Yves Tinevez

commit sha f68c631368c69a7a4ee183e99b24d45a32cc64c7

Change examples.

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Jean-Yves Tinevez

commit sha 90e569f572490115abba20c6cb5d61c423ff8295

Fix an error in the IoU tracker caused by *signed* area.

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Jean-Yves Tinevez

commit sha d0af967d7c9b756f167a84272761ca194608868e

Rename the IoU tracker to Overlap tracker. Let's make it clearer to end-users.

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Jean-Yves Tinevez

commit sha 3b3064728e598df0f534698743d369148bfb0e41

Enable the discplu config button in the GUI after loading.

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issue commentfiji/fiji

ROI from Analyze Particles... fill different in -macro mode vs -batch mode

I can reproduce with an up-to-date Fiji. This may be an issue with imagej-launcher, imagej-legacy or ij1-patcher. @hinerm @ctrueden any ideas?

rgaiacs

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issue openedfiji/Trainable_Segmentation

Closing Weka GUI Chooser started from Trainable Weka Segmentation ends ImageJ2

Hello, hope everyone is well.

There seems to be an issue with closing the Weka GUI Chooser, when started from the segmentation plugin:

Bug: Exiting the Weka GUI Chooser started by the Trainable Weka Segmentation Plugin in ImageJ2 exits ImageJ2 and all open files instead of the Weka GUI Chooser window only

Example:

// open the ImageJ2 Interactive Interpreter (CTRL+J)
// and run a copy of this code (CTRL+R)
run("Blobs (25K)");
run("Trainable Weka Segmentation");
selectWindow("Trainable Weka Segmentation v3.2.34");
call("trainableSegmentation.Weka_Segmentation.launchWeka");

Description The example code will open the Weka GUI Chooser window from the Trainable Weka Segmentation. Interestingly, the close button from the Window itself is non-functional, i.e. the window doesn't close and can't be closed without restarting ImageJ2. If you now want to exit this window (CTRL+E), you'll get a confirmation dialog, prompting you to close "this window" However, this will acutally exit ImageJ2 and all dependentwithout further confirmation.

Expected behaviour: The Weka GUI Chooser window should close, when exiting (command) or closing (clicking) the window.

Versions: Microsoft Windows [Version 10.0.19042.685] ImageJ 2, 1.53g with Java 1.8.0_172 (64-bit) Trainable Weka Segmentation 3.2.34 Weka GUI Chooser 3.9.4

Is this a Weka GUI Chooser issue (calling a global exit function) or a Trainable Weka Segmentation issue (forwarding the local exit function call) or perhaps a combination of the two?

Chris

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fork ZhaoJK/AnalyzeSkeleton

ImageJ/Fiji plugin to analyze 2D and 3D skeleton images

http://fiji.sc/AnalyzeSkeleton

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fork mohamedhelmy1531/Jama

OBSOLETE; see http://central.maven.org/maven2/gov/nist/math/jama/1.0.3/

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issue openedfiji/fiji

ROI from Analyze Particles... fill different in -macro mode vs -batch mode

Wayne Rasband said that https://forum.image.sc/t/imagej-fill-in-macro-mode-vs-batch-mode/47313 might be related with Fiji. Can I have some help to resolve it? Thanks!

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startedfiji/fiji

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issue commentfiji/fiji

import using image sequence runs bio-format importer

@pedrolagomarsino do you still see this issue?

I cannot reproduce, I tried with both ij-1.53c.jar (included in an up-to-date Fiji) and with the daily build (1.53h32).

pedrolagomarsino

comment created time in 12 days

issue commentfiji/dockerfiles

Error running update

Using the make file:

[jamoore@idr1-slot2 fiji-dockerfiles]$ make fiji-openjdk-8
cd fiji-openjdk-8 && docker build -t fiji/fiji:fiji-openjdk-8 .
Sending build context to Docker daemon  5.632kB
Step 1/15 : FROM openjdk:8
 ---> 82f24ce79de6
...
The command '/bin/sh -c ./entrypoint.sh --headless --ij2 --console --run ./demo.py 'name="test"'' returned a non-zero code: 1
make: *** [fiji-openjdk-8] Error 1

If I add a --no-cache to that (which I likely should anyway in the Makefile), I still end with the same exception:

Step 15/15 : RUN ./entrypoint.sh --headless --ij2 --console --run ./demo.py 'name="test"'
 ---> Running in 2a665fe014e6
Jan 08, 2021 5:11:16 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
Error while executing the main() method of class 'net.imagej.Main':
java.lang.IllegalArgumentException: Invalid service: sc.fiji.filamentdetector.gui.GUIStatusService
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:278)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:229)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:192)
	at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:164)
	at org.scijava.Context.<init>(Context.java:278)
	at org.scijava.Context.<init>(Context.java:234)
	at org.scijava.Context.<init>(Context.java:174)
	at org.scijava.Context.<init>(Context.java:160)
	at net.imagej.ImageJ.<init>(ImageJ.java:77)
	at net.imagej.Main.main(Main.java:54)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:291)
	at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:198)
	at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:89)
Caused by: java.lang.NullPointerException
	at java.util.ArrayList.addAll(ArrayList.java:583)
	at org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:193)
	at org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:163)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:315)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:267)
	... 16 more
The command '/bin/sh -c ./entrypoint.sh --headless --ij2 --console --run ./demo.py 'name="test"'' returned a non-zero code: 1
make: *** [fiji-openjdk-8] Error 1
BioinfoTongLI

comment created time in 12 days

issue commentfiji/dockerfiles

Error running update

@joshmoore

and trying to build @BioinfoTongLI's Dockerfile:

I believe this is due to some drift in the older Fiji that is living in the fiji-openjdk-8 image. You can produce the same output without tracking the BigStitcher site, but I believe the update is actually successful. Subsequent updates (with or without BigSticher) appear to be successful:

image

Trying to build a new image I still see:

How are you building the new image? Starting from the current fiji-opendjk-8 I can't reproduce this issue, it works as intended:

image

But not sure how you got to your cb35fa5d2c4e image?

BioinfoTongLI

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fork chuvanmai/Stitching

Fiji's Stitching plugins reconstruct big images from tiled input images.

http://imagej.net/Stitching

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Jean-Yves Tinevez

commit sha 91a519e841db20e1dea4c48554cd62156364666e

Add David Legland JavaGeom library as a dependency.

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Jean-Yves Tinevez

commit sha a0d50f7dca0649aebe65d1a5c182f17ac993c430

A tracker based on intersection-over-union. Initially it was in the TrackMate-StarDist repo, but it makes more sense to have it here instead.

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Jean-Yves Tinevez

commit sha 07be30c8dab7a26698b1d6c1ea82c5b6363565ce

Change the text on the button to save display settings to user default file. Make it clearer to get what this button does.

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