nathanieljevans cyclicIF_registration issues

nathanieljevans / cyclicIF_registration

Registration pipeline for cyclic immuno-fluorescence.

MIT License

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issues

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Edge cores being cutoff

#29 nathanieljevans opened 3 years ago
0
segmentation identifies "core" bounding boxes on image edge that aren't there

#28 nathanieljevans opened 3 years ago
1
Overlapping segmented core bounding boxes

#27 nathanieljevans opened 3 years ago
0
Occasional core registrations fail

#26 nathanieljevans opened 3 years ago
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`restich_cores.py` failing

#25 nathanieljevans opened 3 years ago
3
Relabel core components to appear sequentially

#24 nathanieljevans opened 4 years ago
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use the Fast (E) drive or work directly of the RDS folder

#23 nathanieljevans opened 4 years ago
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only use local config file in both pipeline (local) and libraries/scripts (repo)

#22 nathanieljevans opened 4 years ago
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argument issues when scene name is None

#21 nathanieljevans opened 4 years ago
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multiple core objects are assigned to the same cluster

#20 nathanieljevans opened 4 years ago
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images need to be re-stitched after registration

#19 nathanieljevans closed 4 years ago
1
set up [and document] pipeline on mills workstation

#18 nathanieljevans opened 4 years ago
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Need user readable option to track core labels from original image

#17 nathanieljevans closed 4 years ago
2
manual quality control prior to core re-stitching

#16 nathanieljevans closed 4 years ago
3
notebook results visualization needs option to assign round-channel

#15 nathanieljevans closed 4 years ago
1
provide choice on which round to use as fixed image for registration

#14 nathanieljevans opened 4 years ago
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registration evaluation between all rounds

#13 nathanieljevans opened 4 years ago
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color channel small shift

#12 nathanieljevans opened 4 years ago
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unregisterd core .tif should be deleted after registration

#11 nathanieljevans opened 4 years ago
1
k-means-constrained failing - `There was an issue with the min cost flow input.`

#10 nathanieljevans closed 4 years ago
2
aggregated_results.csv - high missingness

#9 nathanieljevans closed 4 years ago
1
aggregated_results.py: `core` and `component` don't match

#8 nathanieljevans closed 4 years ago
1
R0 results not included in `aggregated_results.csv`

#7 nathanieljevans closed 4 years ago
1
tune registration

#6 nathanieljevans opened 4 years ago
1
screen core components for artifacts prior to across-round matching

#5 nathanieljevans opened 4 years ago
2
tune core segmentation

#4 nathanieljevans opened 4 years ago
1
core isolation includes artifacts and multiple nearby components

#3 nathanieljevans closed 4 years ago
1
registered core naming convention - maintain current style

#2 nathanieljevans opened 4 years ago
0
local registration mask for QC

#1 nathanieljevans opened 4 years ago
0