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mdoube/BoneJ 25

A collection of plugins for bone image analysis in ImageJ

bonej-org/BoneJ2 14

Plugins for bone image analysis

mdoube/fiji 1

Fiji Is Just ImageJ

fiji/pQCT 0

Fiji plugins for pQCT image analysis.

mdoube/bone-macros 0

Collection of bone- and BoneJ-related ImageJ macros and scripts

mdoube/BoneJ2 0

BoneJ2 - the next gen version of BoneJ in development

mdoube/densityDistributionHowTo 0

The instructions for using density distribution ImageJ plug-in, which is included in boneJ

mdoube/downloads 0

Code the TBL has made public with publications

mdoube/drishti 0

Drishti

mdoube/pom-scijava 0

Friendly base POM for all SciJava-based software

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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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 commentnci/drishti

Can't load *.mask.pvl.nc file created by Drishti Paint into Drishti Render

Hi Daurica, The rawmask file stores the mask values, so if the mask values you have chosen are closer to 0 i.e. 1,2,3,4... etc, then you will have to move your transfer function closer to the left side - closer to 0. If you don't want to do that then you can just reimport the rawmask volume (rawmask.pvl.nc.001 file) using DrishtiImport - this will remap the values between min and max.

Cheers, Ajay

On Sat, Jan 16, 2021 at 10:52 PM Daurica notifications@github.com wrote:

Hi, I have a similar problem.

I exported .rawmask, however file.rawmask doesn't seem to be uploaded in Drishti, and file.rawmask.pvl.nc gives me a blank volume, and mix tag command doesn't seem to be doing anything. I was wondering if I need to be in hires mode for that? If so, as soon as I press F2 Drishti crashes..

Hope for some advice and thanks in advance! Cheers

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/nci/drishti/issues/39#issuecomment-761550955, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABMVVLUZ526UY4BGLSSNE7DS2F4YDANCNFSM4I5AGJHQ .

timchaston

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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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push eventfiji/TrackMate

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

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

commit sha 4ab961e60c2727abebdef624b4a46300819f5173

Code style changes.

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Jean-Yves TINEVEZ

commit sha 19880cc41b9aa95d326a98457d2d8ab785df12ab

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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issue commentnci/drishti

Can't load *.mask.pvl.nc file created by Drishti Paint into Drishti Render

Hi, I have a similar problem.

I exported .rawmask, however file.rawmask doesn't seem to be uploaded in Drishti, and file.rawmask.pvl.nc gives me a blank volume, and mix tag command doesn't seem to be doing anything. I was wondering if I need to be in hires mode for that? If so, as soon as I press F2 Drishti crashes..

Hope for some advice and thanks in advance! Cheers

timchaston

comment created time in 4 days

startedekmett/codex

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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

commit sha 0667395bcac20e5d7a371ac9f468522c74367d59

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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Mark Hiner

commit sha 75755497599c22faeb0948d4a9a113d31e46c4ce

Bump to pom-scijava 30.0.0

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startedfission-suite/ipfs-haskell

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startedOpenZeppelin/openzeppelin-contracts

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Mark Hiner

commit sha 207341080c332b395668d51f015416b94969e382

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

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tagij1-patcher-1.2.0

Extension points for ImageJ 1.x via runtime patching to support (limited) headless operation and ImageJ2's legacy layer

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Mark Hiner

commit sha 00d9ae3f8e174ecc80fa05058123ecf8b98e1fc8

Bye bye 2020!

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Mark Hiner

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Mark Hiner

commit sha 54c3af15afb16986c7937088a8b753ceba45327f

Update to ij 1.53d

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tagimagej-common-0.34.0

ImageJ core data model

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Mark Hiner

commit sha bf754cbe469f604b126bf398120b09373cf955e4

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

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Mark Hiner

commit sha 7b4576adb87a2f6da00ee8a253eb0330d9d238b3

The end of 2020!

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