Crawling the web to learn invaluable lessons about the majesty of nature's endangered critters and also to pass our Data Science class
Automatically exported from code.google.com/p/blinker
Crawling the web to learn invaluable lessons about the majesty of nature's endangered critters and also to pass our Data Science class
Fiji Is Just ImageJ
created tagimglib/imglib2-roi
Regions of interest (ROIs) and labelings for ImgLib2
created time in 5 hours
push eventimglib/imglib2-roi
commit sha f1e5daae75cab827790293b0bd9c9859f160d7c8
Bump to next development cycle Signed-off-by: Mark Hiner <hinerm@gmail.com>
push time in 5 hours
push eventimglib/imglib2-roi
commit sha 39e16ef051e1ed776059fb4728b6cf5f8bc237cd
Bye bye 2020!
push time in 5 hours
push eventimglib/imglib2-roi
commit sha 4e80eb5511d4b51eef932b0563a27ab49dbb9631
Increase minor version 96f454cb5f6f506825b69d24149dc997ea5e4c31 adds new API
push time in 5 hours
push eventimglib/imglib2-roi
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.
push time in 5 hours
issue commenttrakem2/TrakEM2
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 The PR may be a bit outdated, but it does exactly that.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.
comment created time in 5 hours
pull request commenttrakem2/TrakEM2
@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.
comment created time in 5 hours
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.
closed time in 14 hours
gitlabspy
issue commenttrakem2/TrakEM2
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 The PR may be a bit outdated, but it does exactly that.
comment created time in 21 hours
push eventfiji/fiji-lib
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.
push time in a day
issue commenttrakem2/TrakEM2
@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()?
comment created time in a day
issue commenttrakem2/TrakEM2
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?
comment created time in a day
issue commenttrakem2/TrakEM2
Polylineis 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.
comment created time in a day
issue commenttrakem2/TrakEM2
@hinerm wrote:
the
ini.trakem2.display.Polylineclass is no longer present in SNT.
Polyline is part of TrakEM2.
comment created time in a day
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.
comment created time in a day
PR opened imagej/imagej-updater
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
pr created time in a day
issue commenttrakem2/TrakEM2
@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.
comment created time in a day
issue openedtrakem2/TrakEM2
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.
created time in a day
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
comment created time in 2 days
push eventfiji/TrackMate
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.
commit sha e58971fec52104635831dc00545e3e0a6eba5172
Don't sample SpotRoi over singleton dimension.
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.
commit sha 41262ae85007c1923142f88b5f6466084c4fe6bd
Utility to reslice an ImgPlus at frame and channel. Used repeatingly in TrackMate, but calling deprecated methods.
commit sha d317ce5d6f3bdb292ff52d2430e9e3179595bcf1
Don't rely on removed TMUtils method to find z-axis.
commit sha 12a01fe073f49badb11d06cbd729b5d0d5c6c7b6
Remove deprecation warnings due to the use of HyperSliceImgPlus.
commit sha 95fd4dee0ee480176ad6431866f4c2a0486ee88f
Use the util to get a spot iterable in the spot intensity analyzer.
commit sha a3659d8980e293dc0be19e8e67ba4e241f29e989
Don't use methods removed in TMUtils to find an axis.
commit sha 4e1dad5b069b0164dfcb86eb785c43f7259077cc
Update AbstractSemiAutoTracker so that it does not rely on deprecated code.
commit sha fa25db558468cacdd140f21504cb1ff6a5e8bdf5
Update the LAP frame-to-frame linker so that it does not use deprecated code.
commit sha 4ab961e60c2727abebdef624b4a46300819f5173
Code style changes.
commit sha 19880cc41b9aa95d326a98457d2d8ab785df12ab
Rework NN tracker so that it does not use deprecated code.
push time in 3 days
push eventfiji/fiji
commit sha ff79d46a26380a0715b54ea648c9526bdc578fba
Bump to next development cycle Signed-off-by: Mark Hiner <hinerm@gmail.com>
push time in 4 days
push eventfiji/fiji
commit sha 3dabdf0a1c6a566ece7170a5b92530489a550153
Bye bye 2020!
push time in 4 days
startedfiles-community/Files
started time in 5 days
push eventfiji/fiji
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
push time in 5 days
push eventimagej/imagej
commit sha 0667395bcac20e5d7a371ac9f468522c74367d59
Bump to next development cycle Signed-off-by: Mark Hiner <hinerm@gmail.com>
push time in 5 days
created tagimagej/imagej
:sparkler: Open scientific N-dimensional image processing :microscope:
created time in 5 days
push eventimagej/imagej
commit sha 18059f9cc540057a4060e1f5f16d552dc0e39109
Bye bye 2020!
push time in 5 days
push eventimagej/imagej
commit sha 6896c8106702aba398f58e3cf7add48e13ac171c
Update snapshot version
push time in 5 days