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Stephan Preibisch StephanPreibisch HHMI Janelia Ashburn, VA, USA http://www.preibisch.net

nicost/uScopeControl 36

A hub to start the next generation of Microscope Control Software

saalfeldlab/render 22

Render transformed image tiles

StephanPreibisch/FourierConvolutionCUDALib 11

Implementation of 3d non-separable convolution using CUDA & FFT Convolution

PreibischLab/multiview-simulation 10

Code for simulating a multi-view acquisition including attenuation, convolution, reduced sampling and poission noise

StephanPreibisch/SeparableConvolutionCUDALib 5

Implementation of 1/2/3d separable convolution using CUDA

jries/Lemming 4

The ultimate superresolution software package

StephanPreibisch/imglib2-introduction 3

Some simple examples of imglib2 code, sample images, and presentation

JaneliaSciComp/SongExplorer 2

deep learning for acoustic signals

kephale/skyview 1

Python interface for SciView

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Friedrich Preusser

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Add files via upload updated color scale for figure 1

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created tagbigdataviewer/bigdataviewer-vistools

tagbigdataviewer-vistools-1.0.0-beta-27

Helpers to use BigDataViewer as a quick visualization tool in other projects.

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tpietzsch

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Bump to next development cycle Signed-off-by: tpietzsch <tobias.pietzsch@gmail.com>

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tpietzsch

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Update license headers

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tpietzsch

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Bump to pom-scijava 30.0.0 and bigdataviewer-core 10.2.0

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tpietzsch

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Simplify handling of BdvOptions.is2D()

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delete branch : 2d

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tpietzsch

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Bump to next development cycle Signed-off-by: tpietzsch <tobias.pietzsch@gmail.com>

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created tagbigdataviewer/bigdataviewer-core

tagbigdataviewer-core-10.2.0

ImgLib2-based viewer for registered SPIM stacks and more

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tpietzsch

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Update license headers

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tpietzsch

commit sha 585d8f098fb0e0961775ec492f2c851a3a878c6b

POM: bump parent to pom-scijava 30.0.0

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pull request commentbigdataviewer/bigdataviewer-core

improve support for modern scaled high-dpi LAFs

FYI if you need to use custom colors for different themes (light/dark), there is some new documentation online that could be interesting for you: https://www.formdev.com/flatlaf/how-to-customize/#application_properties

There is also a UI Defaults Inspector available, which might be useful for development: https://github.com/JFormDesigner/FlatLaf/tree/master/flatlaf-extras#ui-defaults-inspector

axtimwalde

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Mark Hiner

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Bump imglib2-roi -> 0.11.0

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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

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Increase minor version 96f454cb5f6f506825b69d24149dc997ea5e4c31 adds new API

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Mark Hiner

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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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issue commentPreibischLab/BigStitcher

Problem stitching mosaic of oib Olympus files

Hi @hoerldavid

The whole dataset is 39.5 GB so I might be able to send the full thing... Yea, here it is:

https://saco.csic.es/index.php/s/qLK2wJ4bsiJyYsF

Let me know if you need any more info and thanks a lot!

A

auesro

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PR opened trakem2/TrakEM2

Pom scijava 30.0.0

Closes #27

+16 -18

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Mark Hiner

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Bump component version multiview-reconstruction -> 0.9.3

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pull request commentPreibischLab/multiview-reconstruction

Bump to pom-scijava 30.0.0

@StephanPreibisch if you're OK with this change can you merge and cut a new release? Then I'll get it into a new pom-scijava.

hinerm

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PR opened PreibischLab/multiview-reconstruction

Bump to pom-scijava 30.0.0
  • Remove pinned versions
  • Update package imports
+2 -5

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Tom Burke

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Change set usage

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created repositoryjoshmoore/NGFF-GBI-2021-Workshop

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issue commentPreibischLab/BigStitcher

Problem stitching mosaic of oib Olympus files

Alternatively: if your stacks are in individual files and you can reproduce the problem with a subset of them, you could of course also send that.

auesro

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issue commentPreibischLab/BigStitcher

Problem stitching mosaic of oib Olympus files

Hi @auesro ,

Judging from the output I assume it has to do something with the Olympus file format (we have not tested that AFAIK). In the end, I feel that the quickest way to find a fix here would be if you could provide us with an example dataset from your microscope so we can do some debugging.

I assume that this dataset is ~20GB per timepoint - would it be feasible for you to upload one timepoint somewhere?

Best, David

auesro

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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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