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Curtis Rueden ctrueden UW-Madison LOCI Wisconsin, USA https://restlesscoder.net Software architect at LOCI

axtimwalde/mpicbg 44

Fiji module for image transformation and related algorithms

CellProfiler/CellProfiler-plugins 33

Community-contributed and experimental CellProfiler modules.

bonej-org/BoneJ2 14

Plugins for bone image analysis

ctrueden/jcurses-maven 10

Fork of Java Curses 0.9.5 that builds using Maven and CMake

CellProfiler/notebooks 6

Jupyter notebooks for CellProfiler and friends

ctrueden/dotfiles 4

My configuration files

ctrueden/bioformats 2

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment (particularly UW-Madison LOCI and Glencoe Software). Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

ctrueden/ctr-scripts 2

My personal scripts

ctrueden/finite-state-machines 2

Nondeterministic Finite Automaton Simulator

ctrueden/contrib-hacker 1

Hack your GitHub contributions calendar. UNFINISHED

startedcgohlke/imagecodecs

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Mark Hiner

commit sha 472bcc4a1425c84ba7b731bb39d321749a32c224

Bump imglib2-roi -> 0.11.0

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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

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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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Mark Hiner

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Bump TrakEM2 -> 1.3.5

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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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ImageJ plugin for morphological data mining, 3D modeling and image stitching, registration, editing and annotation.

https://imagej.net/TrakEM2

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Mark Hiner

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Bump component version multiview-reconstruction -> 0.9.3

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created repositoryjoshmoore/NGFF-GBI-2021-Workshop

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created repositorymicroscopepony/idr-montage

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created repositorymicroscopepony/idr-count-publications

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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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startedjzy3d/jzy3d-api

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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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fork jburel/skan

Python module to analyse skeleton (thin object) images

https://jni.github.io/skan

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Software for the reconstruction of multi-view microscopic acquisitions like Selective Plane Illumination Microscopy (SPIM) Data

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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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Jan Eglinger

commit sha f6d8749965411a07c9ec96029ad2991620626a1a

Fix Types.raw for GenericArrayType Also add minimal test for array types with generics. See https://github.com/scijava/scijava-common/issues/415

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Jan Eglinger

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TypesTest: test for array types with generics

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Nicolas Chiaruttini

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adds test for string to array conversion in command

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Mark Hiner

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Bump pom-scijava to 30.0.0

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Jan Eglinger

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Improve error message for missing required inputs Human-friendly names can be registered at runtime by calling ObjectService#addHumanFriendlyName(Class, String).

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Fix Types.raw for GenericArrayType Also add minimal test for array types with generics. See https://github.com/scijava/scijava-common/issues/415

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Jan Eglinger

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TypesTest: test for array types with generics

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Nicolas Chiaruttini

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adds test for string to array conversion in command

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Mark Hiner

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Bump pom-scijava to 30.0.0

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Jan Eglinger

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ScriptService: add getScript(String,String) signature This makes it easier to retrieve a ScriptInfo object from a script string (without going via File). Closes #389.

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Jan Eglinger

commit sha f6d8749965411a07c9ec96029ad2991620626a1a

Fix Types.raw for GenericArrayType Also add minimal test for array types with generics. See https://github.com/scijava/scijava-common/issues/415

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Jan Eglinger

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TypesTest: test for array types with generics

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Nicolas Chiaruttini

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adds test for string to array conversion in command

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Mark Hiner

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Bump pom-scijava to 30.0.0

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Add support for #@import directive

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Fix Types.raw for GenericArrayType Also add minimal test for array types with generics. See https://github.com/scijava/scijava-common/issues/415

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Jan Eglinger

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TypesTest: test for array types with generics

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Nicolas Chiaruttini

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adds test for string to array conversion in command

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Mark Hiner

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Bump pom-scijava to 30.0.0

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Fix javadoc of ObjectIndex Remove redundant paragraph.

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Fix Types.raw for GenericArrayType Also add minimal test for array types with generics. See https://github.com/scijava/scijava-common/issues/415

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Jan Eglinger

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TypesTest: test for array types with generics

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Nicolas Chiaruttini

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adds test for string to array conversion in command

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Mark Hiner

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Bump pom-scijava to 30.0.0

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Jan Eglinger

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DefaultWidgetModel: check for null choicesList Let's fail fast and return null when item.getChoices() returns null.

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