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Crawling the web to learn invaluable lessons about the majesty of nature's endangered critters and also to pass our Data Science class

apal4/blinker 0

Automatically exported from code.google.com/p/blinker

apal4/cs638project 0

Crawling the web to learn invaluable lessons about the majesty of nature's endangered critters and also to pass our Data Science class

apal4/fiji 0

Fiji Is Just ImageJ

created tagimglib/imglib2-roi

tagimglib2-roi-0.11.0

Regions of interest (ROIs) and labelings for ImgLib2

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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 4e80eb5511d4b51eef932b0563a27ab49dbb9631

Increase minor version 96f454cb5f6f506825b69d24149dc997ea5e4c31 adds new API

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Mark Hiner

commit sha e7f6f0cc8561d00736b665aa686ef6d199b58abd

Bump pom-scijava to 30.0.0 RealIntervals now validate their own dimensions, so we do not have to add a layer of checking on top.

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issue commenttrakem2/TrakEM2

Update pom-scijava to 30.0.0

Yes! see #25 (07d67a9?diff=split&w=1). The PR may be a bit outdated, but it does exactly that.

@tferr oh perfect. I opened https://github.com/trakem2/TrakEM2/pull/28 which includes your changes and updates the pom as well, now that we have something to pin to.

hinerm

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pull request commenttrakem2/TrakEM2

Pom scijava 30.0.0

@acardona @axtimwalde

This PR includes and can replace https://github.com/trakem2/TrakEM2/pull/25

Can you merge this and cut a new minor release? Then I can make a new pom-scijava and get everything into Fiji.

hinerm

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PR opened trakem2/TrakEM2

Pom scijava 30.0.0

Closes #27

+16 -18

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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

issue commenttrakem2/TrakEM2

Update pom-scijava to 30.0.0

Yes! see #25 (https://github.com/trakem2/TrakEM2/pull/25/commits/07d67a947fd7c23d2b608c4b46b55f50338482cf?diff=split&w=1). The PR may be a bit outdated, but it does exactly that.

hinerm

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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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issue commenttrakem2/TrakEM2

Update pom-scijava to 30.0.0

@tferr can you suggest an alternative? Or can we re-introduce that method?

I am assuming the individual X-Y-Z methods can be looped over from 0..result.size()?

hinerm

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issue commenttrakem2/TrakEM2

Update pom-scijava to 30.0.0

https://github.com/trakem2/TrakEM2/blob/94e44580ebecafe036aeb96fa3150b7e4fa6f7af/src/main/java/ini/trakem2/display/Polyline.java#L716

This can be replaced by result.size().

https://github.com/trakem2/TrakEM2/blob/94e44580ebecafe036aeb96fa3150b7e4fa6f7af/src/main/java/ini/trakem2/display/Polyline.java#L717

That one is more difficult. The getXYZUnscaled() method was removed here:

https://github.com/morphonets/SNT/commit/8f74838884911f4276b09764372d277378872ba4#diff-9d18d39571ccc3273052cc8eb8a38f88b03cb2ef6edccde1f06956dab28288ae

@tferr can you suggest an alternative? Or can we re-introduce that method?

hinerm

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issue commenttrakem2/TrakEM2

Update pom-scijava to 30.0.0

Polyline is part of TrakEM2.

argh. Of course, thank you. Polyline itself needs its imports updated to the new packages:

import sc.fiji.snt.Path;
import sc.fiji.snt.SearchInterface;
import sc.fiji.snt.SearchProgressCallback;
import sc.fiji.snt.TracerThread;

And these lines need to be updated for changed API/field visibility.

hinerm

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issue commenttrakem2/TrakEM2

Update pom-scijava to 30.0.0

@hinerm wrote:

the ini.trakem2.display.Polyline class is no longer present in SNT.

Polyline is part of TrakEM2.

hinerm

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pull request commentimagej/imagej-updater

extend error message with a link to the forum

How about creating a new topic ImageJ FAQ on the forum, where we can group frequently asked questions like this one, and then link to it with a more concise link?

Related: we used to have https://imagej.net/FAQ as well, but it's currently still read-only, and will likely take a while before the wiki is fully migrated.

haesleinhuepf

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PR opened imagej/imagej-updater

extend error message with a link to the forum

Hi @frauzufall, @ctrueden,

I would like to add a link to the forum to an error message. We are repeatedly answering that question on the forum and I think it might help to have that short-cut directly in the error message.

Let me know what you think!

Cheers, Robert

+2 -1

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issue commenttrakem2/TrakEM2

Update pom-scijava to 30.0.0

@axtimwalde @acardona can one of you make this change? I do not have commit rights and am not sure how Polyline usage should be updated.

hinerm

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issue openedtrakem2/TrakEM2

Update pom-scijava to 30.0.0

As of pom-scijava 30.0.0, [the Simple_Neurite_Tracer] dependency](https://github.com/trakem2/TrakEM2/blob/94e44580ebecafe036aeb96fa3150b7e4fa6f7af/pom.xml#L218-L226) can now be updated to org.morphonets:SNT.

Some migration is necessary as TrakEM2 as the ini.trakem2.display.Polyline class is no longer present in SNT.

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issue commentimagej/imagej

Create a Windows installer for ImageJ2/Fiji

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/fiji-updater-problem-flimj-installation-error/47560/5

ctrueden

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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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commit sha 12a01fe073f49badb11d06cbd729b5d0d5c6c7b6

Remove deprecation warnings due to the use of HyperSliceImgPlus.

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commit sha 95fd4dee0ee480176ad6431866f4c2a0486ee88f

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

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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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commit sha fa25db558468cacdd140f21504cb1ff6a5e8bdf5

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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created tagfiji/fiji

tagfiji-2.2.0

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

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Mark Hiner

commit sha ff79d46a26380a0715b54ea648c9526bdc578fba

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

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Mark Hiner

commit sha 3dabdf0a1c6a566ece7170a5b92530489a550153

Bye bye 2020!

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startedfiles-community/Files

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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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Mark Hiner

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

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created tagimagej/imagej

tagimagej-2.2.0

:sparkler: Open scientific N-dimensional image processing :microscope:

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Mark Hiner

commit sha 18059f9cc540057a4060e1f5f16d552dc0e39109

Bye bye 2020!

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Mark Hiner

commit sha 6896c8106702aba398f58e3cf7add48e13ac171c

Update snapshot version

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