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Tom Kazimiers tomka kazmos GmbH Dresden, Germany Developer of CATMAID, a tool for collaborative connectome reconstruction and analysis and more.

tomka/cliaspora 9

A command line client for the distributed social network Diaspora.

schlegelp/CATMAID-to-Blender 6

Plugin for Blender to interface with CATMAID Server and Pull Data

tomka/copo 5

This project is the result of my minor thesis at TU Dresden, Germany. Now it is made public, GPLv2 licenced and worked on once in a while. It is basically an implementation of of Paul Fearings "Computer modelling of fallen snow" -- most of it. Parts of the folder structure will be changed, namely the dependencies folder - the binaries will be excluded.

aschampion/schemer 3

A database schema migration library with DAG dependencies

BrainCircuitsIO/circuitmap 3

Django application serving data for synapse-guided circuit mapping in CATMAID

fzadow/tileserver 2

Tileserver

imagej/imagej.github.io 2

GitHub Pages for ImageJ

tomka/cmaked 2

A git-svn mirror of cmaked repository of http://www.dsource.org/projects/cmaked

ntj/fraktionstool 1

Ein Tool zur Verwaltung von Vorhaben in der kommunalen Fraktionsarbeit

issue commentgoogle/neuroglancer

define get_skeleton() in SkeletonSource for custom data

Turns out the skeleton example was broken --- I just fixed it.

get_skeleton is called by the Python Neuroglancer code when the client requests a skeleton --- your own code doesn't need to call it directly.

hash-ir

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push eventgoogle/neuroglancer

Jeremy Maitin-Shepard

commit sha d91a20a00b6809eaa7487a04eebaf4f2c9f2d94a

fix(python): add SkeletonSource error checking and fix skeleton example Fixes #277

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issue closedgoogle/neuroglancer

define get_skeleton() in SkeletonSource for custom data

I am running a skeleton example on custom data inspired by example_skeleton.py. I implemented the get_skeleton() method of SkeletonSource but I didn't find its use anywhere in the example. I want to know how I can forward my custom skeleton data to the viewer source?

In the skeleton example, the dummy segmentation data is provided in a LocalVolume and a SkeletonSource object is just instantiated without using the get_skeleton() method.

with viewer.txn() as s:
    s.layers.append(
        name='a',
        layer=neuroglancer.SegmentationLayer(
            source=[
                neuroglancer.LocalVolume(
                    data=segmentation, # here
                    dimensions=dimensions,
                ),
                SkeletonSource(dimensions), # here
            ],
            skeleton_shader='void main() { emitRGB(colormapJet(affinity)); }',
            selected_alpha=0,
            not_selected_alpha=0,
            segments=[395750],
        ))

closed time in an hour

hash-ir

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

comment created time in 4 hours

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

comment created time in 4 hours

PR opened trakem2/TrakEM2

Pom scijava 30.0.0

Closes #27

+16 -18

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2 changed files

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created repositoryjoshmoore/NGFF-GBI-2021-Workshop

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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.

closed time in 13 hours

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

comment created time in 20 hours

fork sofroniewn/affinder

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

fork in 21 hours

issue commentgoogle/neuroglancer

Annotations no longer displaying after Ubuntu upgrade

Thanks for the tips. Reinstalling GPU drivers and then rebooting did the trick. Firefox was not working either. For anyone who runs into this problem in the future, chrome://gpu is a good diagnostic. After the fix, this is what that page displays:

chrome-gpu-config_postfix

austinhoag

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push eventfiji/fiji-lib

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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push eventsaalfeldlab/paintera

cmhulbert

commit sha e0cdb0770ae049bb79770774840a23c321e84ac5

target 11, update scijava pom

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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

comment created time in a day

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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startedpmsipilot/docker-compose-viz

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startedsnowpackjs/snowpack

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startedbahmutov/mocked-env

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issue commentgoogle/neuroglancer

Annotations no longer displaying after Ubuntu upgrade

You can also see if Firefox works.

austinhoag

comment created time in a day

issue closedgoogle/neuroglancer

Annotations no longer displaying after Ubuntu upgrade

I recently upgraded to Ubuntu 18.04 and I am seeing a bunch of weird behavior using your client (all clients, actually), all related to WebGL. I'm guessing it's just a missing driver, but I'm not sure how to debug that.

The behavior I can reproduce most easily is that manually added annotations do not show up in a new annotation layer. They are added in the annotation list but do not show up visually. In the rendering tab of the annotation layer I see this error:

ng-webgl-annotation-error

The console does not report any errors. Here is what I see at chrome://gpu:

chrome-gpu-config

I'm not sure which of these Neuroglancer uses. Does that look suspect?

closed time in a day

austinhoag

issue commentgoogle/neuroglancer

Annotations no longer displaying after Ubuntu upgrade

If Chrome determines that your GPU cannot be used, it falls back to its built-in software rendering system called SwiftShader. You can check the WebGL2 tab of webglreport.com to see if swiftshader is listed. Unfortunately SwiftShader has some bugs in its WebGL2 support that prevent Neuroglancer from working properly --- in many cases WebGL will crash completely (shows up as a context lost error in the console), but those shader errors you see are another problem I have observed.

I would suggest that you figure out how to get GPU rendering to work again on your system. Even if Swiftshader worked, it would still be slow. I can't really say exactly how to get your GPU drivers working, but reinstalling the drivers may help.

austinhoag

comment created time in a day

issue openedgoogle/neuroglancer

Annotations no longer displaying after Ubuntu upgrade

I recently upgraded to Ubuntu 18.04 and I am seeing a bunch of weird behavior using your client (all clients, actually), all related to WebGL. I'm guessing it's just a missing driver, but I'm not sure how to debug that.

The behavior I can reproduce most easily is that manually added annotations do not show up in a new annotation layer. They are added in the annotation list but do not show up visually. In the rendering tab of the annotation layer I see this error:

ng-webgl-annotation-error

The console does not report any errors. Here is what I see at chrome://gpu:

chrome-gpu-config

I'm not sure which of these Neuroglancer uses. Does that look suspect?

created time in a day

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

comment created time in a day

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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startedpmndrs/react-three-fiber

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startedlace/vg

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issue openedgoogle/neuroglancer

define get_skeleton() in SkeletonSource for custom data

I am running a skeleton example on custom data inspired by example_skeleton.py. I implemented the get_skeleton() method of SkeletonSource but I didn't find its use anywhere in the example. I want to know how I can forward my custom skeleton data to the viewer source?

In the skeleton example, the dummy segmentation data is provided in a LocalVolume and a SkeletonSource object is just instantiated without using the get_skeleton() method.

with viewer.txn() as s:
    s.layers.append(
        name='a',
        layer=neuroglancer.SegmentationLayer(
            source=[
                neuroglancer.LocalVolume(
                    data=segmentation, # here
                    dimensions=dimensions,
                ),
                SkeletonSource(dimensions), # here
            ],
            skeleton_shader='void main() { emitRGB(colormapJet(affinity)); }',
            selected_alpha=0,
            not_selected_alpha=0,
            segments=[395750],
        ))

created time in a day

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