SainsburyWellcomeCentre / neuro / 52 / 1
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52.1

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Add manual segmentation (#23)

* points to brainrender

* update testing

* refactor

* refactor

* badges

* notes

* initial inj finder commit (#11)

* formatting with black

* add .DS_store to gitignore

* typo

* update imports

* update imports

* deal with no obj path given

* error typo

* move utils too imlib

* remove amap imports

* optional logging to file

* tidy

* registration moved to imlib

* keep largest object

* reduce RAM usage

* remove unnecessary logging args

* adds lesion and track estimation and generic tools

* add missing dir support for cell export

* add missing dir support for cell export

* reduce mem requirements

* remove old code

* remove old code

* refactor scaling

* fix failing heatmap test

* update docs

* ensure output directory exists

* make pixel sizes mandatory

* make pixel sizes mandatory (#17)

* move functionality to imlib

* remove hard coded smoothing

* Refactor (#19)

* make pixel sizes mandatory

* move functionality to imlib

* remove hard coded smoothing

* update docs

* Injectionsite (#20)

* refactors code from SL to import from neuro and imlib only

* moves amap_vis to neuro and removes amap and cellfinder dependencies;

* format with black

* amap_vis

* bump

* remove cellfinder dependency

* cli entry point for fibre track segmentation

* refactor seg tools

* start manual seg

* remove hardocoding in manual region segmentation

* refactor paths

* bump

Co-authored-by: Federico Claudi <federicoclaudi@protonmail.com>
Co-authored-by: stephen <stephen.lenzi@gmail.com>

140 of 764 relevant lines covered (18.32%)

0.18 hits per line

Source Files on job 52.1