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Polaris super consumer #183

Merged
merged 70 commits into from
Apr 19, 2022
Merged

Polaris super consumer #183

merged 70 commits into from
Apr 19, 2022

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elaubsch
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This PR introduces a Polaris "super consumer" that handles spot detection and cell segmentation for singleplex FISH analysis.

  • The consumer that handles spot detection tasks - previously called the PolarisConsumer - has been refactored to the SpotDetectionConsumer.
  • The label detection model has been removed from the segmentation consumer and the channel handling for nuclear and whole-cell segmentation is now done manually.
  • The MAX_SCALE variable has been increased from 3 to 10 to allow for segmentation of 100x images, which are typical for FISH experiments.

@elaubsch
SpotDetection to Polaris app
e85639b
@elaubsch
Add segmentation model to Polaris consumer
efe1797
@elaubsch
Create spot detection consumer
8c45767
@elaubsch
Initial commit of super consumer
958fa73
@elaubsch
Refactor to spot_consumer
df0a3fc
@elaubsch
Fix bugs in consumer output
4d2c7ec
@elaubsch
Refine output
5c05c92
@elaubsch
Add output function for coords only
a20afe3
@elaubsch
Add SpotConsumer
4f14408
@elaubsch
Change spot size
f761508
@elaubsch
Increase MAX_SCALE setting
73a261d
@elaubsch
Fix multi-channel output
632bd60
@elaubsch
Change queue in polaris tests
5e5d267
@elaubsch
Remove polaris consume test
2fb1bee
@elaubsch
PEP8
682bac1
@elaubsch
Remove spots consume test
c066240
@elaubsch
PEP8
8d0cd16
@elaubsch
Fix bug in scale test
828a24c
@elaubsch
Update spot consume test
84c66e7
@elaubsch
Manual 2 model channel wrangling
bda0b23
@elaubsch
Switch output dimensions and refactor label to channels
bb020e7
@elaubsch
Remove label detection tests
42271ba
@elaubsch
Check if channels exists
d814106
@elaubsch
Add channels to test input
b7fdcf0
@elaubsch
Remove dimension from channels
78832af
@elaubsch
Remove label detection model
47520b2
@elaubsch
Update model/app label and cap batch size
3a36f6b
@elaubsch
Fix dimension handling in polaris consumer
098a645
@elaubsch
Spot predict params from settings.py
fdebc5e
@elaubsch elaubsch added the enhancement New feature or request label Mar 30, 2022
msschwartz21
msschwartz21 reviewed Apr 18, 2022
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This looks great! Thanks for all of the hard work!

Let me know what you think about the couple of last comments I left and then I'll approve.

redis_consumer/consumers/polaris_consumer.py Outdated Show resolved Hide resolved
redis_consumer/consumers/polaris_consumer.py Outdated Show resolved Hide resolved
redis_consumer/consumers/polaris_consumer_test.py Show resolved Hide resolved
@elaubsch elaubsch merged commit 90970fc into master Apr 19, 2022
@elaubsch elaubsch deleted the polaris-super-consumer branch April 19, 2022 04:55
@elaubsch elaubsch mentioned this pull request Apr 21, 2022
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@msschwartz21 msschwartz21 msschwartz21 approved these changes

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@elaubsch @msschwartz21