Add all Kim's DevCCFv1 atlases (#441)

* initial work to add Kim DevCCFv1 2024

* fix orientation and resolution

* DevCCFv1 atlases are now fetched online and generated for all timestamps

* skip mesh creation if done already

* removed unnecessary comments

* add options --timepoints and --modality to DevCCF

* add hashes to DevCCF

* last fixups for DevCCF

* add option --decimate-fraction to DevCCF

* DevCCFv1 atlases are named as kim_devccf_mouse_<AGE>_<MODALITY>

* set kim_devccf_mouse atlases as version=3 of kim_dev_mouse

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* make linter happy, remove unused code

* set manifest to ignore atlas_generation/hashes

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* DevCCF: atlas files extracted with pooch.Unzip() are now correctly assigned

* fix reference images being badly converted to tiff

* add option --cached-meshes to DevCCF

---------

Co-authored-by: Carlo Castoldi <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: alessandrofelder <[email protected]>

MANIFEST.in

@@ -11,3 +11,4 @@ graft brainglobe_atlasapi *.py
 prune tests
 prune tutorials
 prune brainglobe_atlasapi/atlas_generation/atlas_scripts/*
+prune brainglobe_atlasapi/atlas_generation/hashes