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Larry Lindsey larrylindsey Seattle, WA

jni/ray 27

Automatic segmentation of electron microscopy volumes

larrylindsey/MatlabCode 2

My personal stash of matlab code. Please excuse the mess.

larrylindsey/arduino-samd5x-motor 1

Arduino support for SAMD5X hardware PDEC functionality

larrylindsey/DynoUSB 1

A 5V USB rectifier project in EagleCAD

larrylindsey/reconstructmergetool 1

Reconstruct Merge Tool

larrylindsey/CATMAID 0

Collaborative Annotation Toolkit for Massive Amounts of Image Data

larrylindsey/catmaidsopnet 0

Catmaid integration module for Sopnet

larrylindsey/CLM_ 0

A collection of plugins written for tasks that may or may not be specific to the Kristen Harris Lab in the Center for Learning and Memory at UT Austin.

larrylindsey/cmake 0

module-based cmake build system

larrylindsey/covid-risk-viz 0

Covid Risk Visualizations, Computed from the New York Times dataset

created tagimglib/imglib2-roi

tagimglib2-roi-0.11.0

Regions of interest (ROIs) and labelings for ImgLib2

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Mark Hiner

commit sha f1e5daae75cab827790293b0bd9c9859f160d7c8

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

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Mark Hiner

commit sha 39e16ef051e1ed776059fb4728b6cf5f8bc237cd

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 The PR may be a bit outdated, but it does exactly that.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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created repositoryjni/affinder

Quickly find the affine matrix mapping one image to another using manual correspondence points annotation

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issue commentsaalfeldlab/render

Render server resource recommendation

re: different sized web services VMs and server-side rendering

Yes, each VM hosts a separate render web services instance and they all connect to one centralized database. I separated the web servers to handle different types of tasks. The small VMs are dedicated to simple data retrieval use - no server-side rendering. The larger VMs are used for server-side rendering. Finally there is a large web services instance on real hardware that provides reliable large scale data access with no (or only very small occasional) server-side rendering.

The main idea is to separate resource intensive server-side rendering from pure data retrieval. The data retrieval services need to be always available while the server-side rendering is "extra-credit". Separating to different hosts means that too many server-side rendering requests won't cause trouble for concurrently running cluster jobs that only need data.

Technically, almost everything can be done server-side (because the same libraries are used) but practically it works best when rendering is done client-side.

  • When a client retrieves tile specs, the mipmap paths (or the ability to derive the paths for a stack) is included. The client then reads the mipmaps directly from network storage (same as the source images).
  • When requesting a scaled down image within a client, the client loads the appropriate mipmap (if available) and then downsamples as needed. Having mipmaps makes this process much faster, but it will still work (slowly) if you don't have mipmaps.
  • When requesting a scaled down image (not tile spec) directly from a server, the server acts just like a client and downsamples in the same way using mipmaps if they are available.
martinschorb

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issue commentsaalfeldlab/render

Render server resource recommendation

re: comprehensive entry package

I like this idea and think a Docker containerized deployment is the best way to set this up. Maybe we can revisit render's current all-in-one Docker example to make it more user friendly and suitable for small scale use.

To determine whether a particular setup is performing well, the easiest thing to do is run some typical jobs (import, match generation, materialize to disk) and then look at the web services access log (jetty_base/logs/<yyyy>-<mm>/<ts>-access.log). The log will show response times for each request which will typically be in the 0 to 5 ms range (20-50 ms for larger requests) if the system is running well.

martinschorb

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issue commentsaalfeldlab/render

Render server resource recommendation

Hi Martin,

re: database hardware architecture ...

Yes, the DB machine needs enough disk storage to hold everything in render and enough memory to hold the data (stacks and match collections) being actively accessed. Theoretically, you can reduce database disk storage requirements by creating bson dumps for inactive stack data, moving the dumps to cheaper "offline" storage, and removing the inactive data from the database. This is a bit of a hassle though, so I've only done it a couple times once I knew we were really done with a large project.

Although it is tempting to co-host the database and the web server, I would not recommend this long-term unless you are managing a fairly small amount of data (in total). I suppose you could start with everything together and separate components later when things grow and break down.

How long do you think you'll need to hold onto the 10k - 1M tile stacks? Are the "one working day" alignments likely to be related to each other (e.g. different parts of the same volume) or are they completely independent projects?

If most/all of your projects are small and independent, then it might make sense to have lots of small (co-located) database + web service deployments where each deployment is dedicated to a project. If instead you need to keep the data around for longer and/or you need to move back and forth between lots of related data, the separate centralized database model is better - this what we do at Janelia and what is also done at the Allen Institute.

martinschorb

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issue openedcatmaid/CATMAID

new node type for treenode table: adjacent to section gap

By checking the table of broken slices, the Treenode Table widget should be able to filter for skeleton treenodes adjacent to broken slices, or whose edge crosses a broken slice.

This would enable swiftly reviewing gap crosses for a given neuron.

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Tom Kazimiers

commit sha 6ec21c32d4979aabf88a13511cfe62bda405cf6c

Export mgmt. command: include tags on connectors in export Previously, only the links to those tags where exported and not the tags themselves, leading to a consistency error during import (if tags where included). This is fixed now.

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Tom Kazimiers

commit sha 8065fbc0931b8a15b27e15d5b8589abbb45227c3

Doc: slightly improve wording in training section The referred to fly nomenclature is now the 'standard fly brain nomenclature', rather than the 'virtual fly brain nomenclature'. This is the intended meaning and avoids confusion with VFB. Thanks to Marta Costa for this suggestion!

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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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startedwahn/rs_pbrt

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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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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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Wayne Rasband

commit sha 2bf338ae80e6ccfc250994beb4e7e3511833bd51

2021.01.16 (1.53h47; Toolbar.setIcon)

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