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Tensorflow segmentation #3461

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merged 65 commits into from
Apr 10, 2019
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8dcc126
integrate first version of tensorflow-js segmentation model
philippotto Nov 16, 2018
a9c32f1
add flood fill and whole viewport prediction
daniel-wer Nov 16, 2018
1a77c16
implement high-perf way of accessing arbitrary cuboid data in front-end
philippotto Nov 16, 2018
d6be4b9
Merge branch 'tensorflow-segmentation' of github.com:scalableminds/we…
philippotto Nov 17, 2018
9d60b9c
fix some things, wand is working again
daniel-wer Nov 17, 2018
9555cef
fix everything
daniel-wer Nov 17, 2018
0845179
copy tf models via webpack
philippotto Nov 17, 2018
abe44ef
upgrade webpack
daniel-wer Dec 5, 2018
17bcbe9
increase node memory
daniel-wer Dec 5, 2018
a0c1905
fix lint, tests
daniel-wer Dec 5, 2018
f6bf73a
Merge branch 'master' of github.com:scalableminds/webknossos into ten…
daniel-wer Dec 5, 2018
33086e5
Merge branch 'master' of github.com:scalableminds/webknossos into ten…
daniel-wer Mar 20, 2019
a7cc6c3
fix model asset path
daniel-wer Mar 20, 2019
9bedea7
Merge branch 'master' of github.com:scalableminds/webknossos into ten…
daniel-wer Mar 25, 2019
26b1e4b
update tensorflowjs to 1.0
daniel-wer Mar 26, 2019
1d10247
move viewport when pressing alt and moving mouse
philippotto Mar 26, 2019
608d84c
Merge branch 'tensorflow-segmentation' of github.com:scalableminds/we…
philippotto Mar 26, 2019
96eb19a
Tensorflow segmentation statistics (#3946)
fm3 Mar 26, 2019
b49010b
adapt tensorflow segmentation to rectangular viewports
daniel-wer Mar 26, 2019
159476b
Merge branch 'tensorflow-segmentation' of github.com:scalableminds/we…
daniel-wer Mar 26, 2019
c21268b
fix lint
daniel-wer Mar 26, 2019
a111f4f
added mean and stdDev fetching route and using it for the magic wand …
MichaelBuessemeyer Mar 26, 2019
b2eb004
applied new formular again
MichaelBuessemeyer Mar 26, 2019
f9f3f9e
fixed lint and flow
MichaelBuessemeyer Mar 26, 2019
fa87e5f
predict for next 5 slices as well
daniel-wer Mar 26, 2019
91a0795
allow tf inference in webworker
philippotto Mar 26, 2019
8eb0752
Merge branch 'tensorflow-segmentation' of github.com:scalableminds/we…
daniel-wer Mar 26, 2019
f86e981
made magic wand tool optional
MichaelBuessemeyer Mar 26, 2019
4ede20c
Merge branch 'tensorflow-segmentation' of github.com:scalableminds/we…
MichaelBuessemeyer Mar 26, 2019
823dbd6
Merge branch 'tensorflow-segmentation' of github.com:scalableminds/we…
philippotto Mar 26, 2019
7baa52d
Merge branch 'tensorflow-segmentation' of github.com:scalableminds/we…
MichaelBuessemeyer Mar 26, 2019
b3dce8f
fix shard in webpack-dev-server mode
daniel-wer Mar 26, 2019
92bfee9
enabled magic wand tool as default
MichaelBuessemeyer Mar 26, 2019
8f3c291
Merge branch 'tensorflow-segmentation' of github.com:scalableminds/we…
MichaelBuessemeyer Mar 26, 2019
e52297c
fix tests
philippotto Mar 26, 2019
2defef9
Merge branch 'tensorflow-segmentation' of github.com:scalableminds/we…
philippotto Mar 26, 2019
c265c84
Merge branch 'tensorflow-segmentation' of github.com:scalableminds/we…
MichaelBuessemeyer Mar 26, 2019
1a71d95
use new segem model, restrict viewport to 100x100 voxel for perf
daniel-wer Mar 26, 2019
5d322c9
Merge branch 'tensorflow-segmentation' of github.com:scalableminds/we…
daniel-wer Mar 26, 2019
5f0dbf9
small perf/cleanup fixes
daniel-wer Mar 26, 2019
9af6f18
merge master into tensorflow-segmentation
fm3 Mar 27, 2019
2ec8d2b
load model from right path
fm3 Mar 27, 2019
4d9403d
only use webworker if offscreencanvas is supported
philippotto Mar 27, 2019
90d1ad2
Merge branch 'master' of github.com:scalableminds/webknossos into ten…
daniel-wer Apr 1, 2019
dab5da6
use 3d-floodfill for magic wand
daniel-wer Apr 1, 2019
eab3909
add and adapt floodfill lib, do 3d floodfill, do tile-based predict a…
daniel-wer Apr 3, 2019
3a2da3a
adapt floodfill to work slice for slice, optimize voxel labeling, rem…
daniel-wer Apr 3, 2019
0276709
add flow to floodfill, fix flow
daniel-wer Apr 3, 2019
8d8b414
add magic wand unlimited mode, will predict next x slices until abort…
daniel-wer Apr 3, 2019
3e6590e
use global tiles instead of viewport local, makes everything easier
daniel-wer Apr 3, 2019
eb8cdf0
update the whole position, so that segments that move out of the view…
daniel-wer Apr 3, 2019
6da5961
fix magic wand for xz and yz planes
daniel-wer Apr 3, 2019
6a2cc69
fix mean,stddev memoization, refactor common code
daniel-wer Apr 3, 2019
457754a
small changes to toast and code
daniel-wer Apr 3, 2019
6d706d1
Merge branch 'master' of github.com:scalableminds/webknossos into ten…
daniel-wer Apr 8, 2019
7dcae93
add new tensorflow model, apply PR feedback #1
daniel-wer Apr 8, 2019
9589321
apply PR feedback #2
daniel-wer Apr 9, 2019
1bfcdcd
update redux-saga and typedefs to 1.0, avoid spawning magic wand twice
daniel-wer Apr 9, 2019
e869fbe
clean up prediction data for old z slices, rename magic wand to autom…
daniel-wer Apr 9, 2019
ec1415c
refactor automatic brushing code into own module
daniel-wer Apr 9, 2019
367eba4
disable magic wand by default
daniel-wer Apr 9, 2019
f1a9e47
Merge branch 'master' of github.com:scalableminds/webknossos into ten…
daniel-wer Apr 9, 2019
d0cd45a
react to zoom changes, amend automatic brush label
daniel-wer Apr 9, 2019
7d1ed27
apply PR feedback #3, use newest model with slightly different normal…
daniel-wer Apr 10, 2019
0b64910
disable automatic brush by default
daniel-wer Apr 10, 2019
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2 changes: 2 additions & 0 deletions conf/messages
Original file line number Diff line number Diff line change
Expand Up @@ -96,6 +96,8 @@ dataSet.dataStore.missing=dataStore missing in the supplied json
dataSet.dataSet.missing=dataSet missing in the supplied json
dataSet.downloadAlreadyRunning=Sample dataset download is already running.
dataSet.alreadyPresent=Sample dataset is already present.
dataSet.noResolutions=Data layer does not contain resolutions
dataSet.sampledOnlyBlack=Sampled data positions contained only black data

dataSource.notFound=Datasource not found on datastore server

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1 change: 1 addition & 0 deletions docker-compose.yml
Original file line number Diff line number Diff line change
Expand Up @@ -99,6 +99,7 @@ services:
- HOME=/root
- CIRCLE_TAG=${CIRCLE_TAG}
- CIRCLE_BUILD_NUM=${CIRCLE_BUILD_NUM}
- NODE_OPTIONS=--max_old_space_size=2048
working_dir: /home/${USER_NAME:-sbt-user}/webknossos
volumes:
- ".:/home/${USER_NAME:-sbt-user}/webknossos"
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2 changes: 2 additions & 0 deletions docs/keyboard_shortcuts.md
Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@ Find all available keyboard shortcuts for webKnossos listed below.
| Key Binding | Operation |
| ----------------------------- | ------------------------------------------- |
| Left Mouse Drag or Arrow Keys | Move |
| Alt + Mouse Move | Move |
| SPACE | Move Forward by a Single Slice |
| Scroll Mousewheel (3D View) | Zoom In And Out |
| Right Click Drag (3D View) | Rotate 3D View |
Expand Down Expand Up @@ -78,6 +79,7 @@ Find all available keyboard shortcuts for webKnossos listed below.
| CTRL + Left Mouse Drag | Add Empty Voxels To Current Cell (in Trace / Brush Mode) |
| Right Mouse Drag | Remove Voxels From Current Cell |
| CTRL + Right Mouse Drag | Remove Voxels From Any Cell |
| Alt + Mouse Move | Move |
| C | Create New Cell |
| W, 1 | Toggle Modes (Move / Trace / Brush) |
| SHIFT + Mousewheel or SHIFT + I, O | Change Brush Size (Brush Mode) |
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