SainsburyWellcomeCentre / cellfinder / 346

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brainreg integration (#142)

* Update dependencies

* lint


* add brainreg registration

* continue brainreg integration

* refactor

* remove group summary

* remove amap references

* remove unused tests

* add reg test

* remove unused code

* remove unused code

* update whattorun

* remove heatmap

* remove neuro depedency

* remove brainio

* remove dependencies

* remove unused code

* update linting

* refactor

* save points

* save points to single directory

* add heatmap

* update summary csv saving

* remove option to save relative structure centres when splitting

* deal with no cells being detected

* update skipping of cell candidate dependent steps

* save json

* remove unused code

* update test scripts

* update reqs

* Update testing

* update requirements

* update testing

* update deployment

* update logging of metadata

* Update testing

* update registration test

298 of 298 new or added lines in 15 files covered. (100.0%)

1591 of 2051 relevant lines covered (77.57%)

3.87 hits per line