diff --git a/registration/0.5.4/README.txt b/registration/0.5.4/README.txt
deleted file mode 100644
index f48879c52c336bb8b003704d8bd63d3445984bb7..0000000000000000000000000000000000000000
--- a/registration/0.5.4/README.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-Registration based only on nuclei/dapi. I got this from Tischi and I am not quite sure if these transformations correspond to '9.9.9/transformations'.
-Replace this folder with 9.9.9, if transformations turn out to be identical.
diff --git a/registration/9.9.9/EM/nuclei_to_remove.csv b/registration/deprecated/EM/nuclei_to_remove.csv
similarity index 100%
rename from registration/9.9.9/EM/nuclei_to_remove.csv
rename to registration/deprecated/EM/nuclei_to_remove.csv
diff --git a/registration/9.9.9/EM/nucleus_exclusion_mask.xml b/registration/deprecated/EM/nucleus_exclusion_mask.xml
similarity index 100%
rename from registration/9.9.9/EM/nucleus_exclusion_mask.xml
rename to registration/deprecated/EM/nucleus_exclusion_mask.xml
diff --git a/registration/9.9.9/notes/registration-strategy.txt b/registration/deprecated/notes/registration-strategy.txt
similarity index 100%
rename from registration/9.9.9/notes/registration-strategy.txt
rename to registration/deprecated/notes/registration-strategy.txt
diff --git a/registration/9.9.9/quality-assessment/compute-registration-quality.R b/registration/deprecated/quality-assessment/compute-registration-quality.R
similarity index 100%
rename from registration/9.9.9/quality-assessment/compute-registration-quality.R
rename to registration/deprecated/quality-assessment/compute-registration-quality.R
diff --git a/registration/9.9.9/quality-assessment/em-fixed-points.txt b/registration/deprecated/quality-assessment/em-fixed-points.txt
similarity index 100%
rename from registration/9.9.9/quality-assessment/em-fixed-points.txt
rename to registration/deprecated/quality-assessment/em-fixed-points.txt
diff --git a/registration/9.9.9/quality-assessment/manually_matched_points.xlsx b/registration/deprecated/quality-assessment/manually_matched_points.xlsx
similarity index 100%
rename from registration/9.9.9/quality-assessment/manually_matched_points.xlsx
rename to registration/deprecated/quality-assessment/manually_matched_points.xlsx
diff --git a/registration/9.9.9/quality-assessment/notes.txt b/registration/deprecated/quality-assessment/notes.txt
similarity index 100%
rename from registration/9.9.9/quality-assessment/notes.txt
rename to registration/deprecated/quality-assessment/notes.txt
diff --git a/registration/9.9.9/quality-assessment/outputpoints.txt b/registration/deprecated/quality-assessment/outputpoints.txt
similarity index 100%
rename from registration/9.9.9/quality-assessment/outputpoints.txt
rename to registration/deprecated/quality-assessment/outputpoints.txt
diff --git a/registration/9.9.9/quality-assessment/transformix.log b/registration/deprecated/quality-assessment/transformix.log
similarity index 100%
rename from registration/9.9.9/quality-assessment/transformix.log
rename to registration/deprecated/quality-assessment/transformix.log
diff --git a/registration/9.9.9/quality-assessment/~$manually_matched_points.xlsx b/registration/deprecated/quality-assessment/~$manually_matched_points.xlsx
similarity index 100%
rename from registration/9.9.9/quality-assessment/~$manually_matched_points.xlsx
rename to registration/deprecated/quality-assessment/~$manually_matched_points.xlsx
diff --git a/registration/9.9.9/scripts/elastix.ijm b/registration/deprecated/scripts/elastix.ijm
similarity index 100%
rename from registration/9.9.9/scripts/elastix.ijm
rename to registration/deprecated/scripts/elastix.ijm
diff --git a/registration/9.9.9/scripts/mask_gut_nuclei.py b/registration/deprecated/scripts/mask_gut_nuclei.py
similarity index 100%
rename from registration/9.9.9/scripts/mask_gut_nuclei.py
rename to registration/deprecated/scripts/mask_gut_nuclei.py
diff --git a/registration/9.9.9/scripts/prepare_image_data.ijm b/registration/deprecated/scripts/prepare_image_data.ijm
similarity index 100%
rename from registration/9.9.9/scripts/prepare_image_data.ijm
rename to registration/deprecated/scripts/prepare_image_data.ijm
diff --git a/registration/9.9.9/scripts/registration_targets/exclude_nuclei_from_table.py b/registration/deprecated/scripts/registration_targets/exclude_nuclei_from_table.py
similarity index 100%
rename from registration/9.9.9/scripts/registration_targets/exclude_nuclei_from_table.py
rename to registration/deprecated/scripts/registration_targets/exclude_nuclei_from_table.py
diff --git a/registration/9.9.9/scripts/registration_targets/move_meds.py b/registration/deprecated/scripts/registration_targets/move_meds.py
similarity index 100%
rename from registration/9.9.9/scripts/registration_targets/move_meds.py
rename to registration/deprecated/scripts/registration_targets/move_meds.py
diff --git a/registration/9.9.9/scripts/registration_targets/set_voxel_size.ijm b/registration/deprecated/scripts/registration_targets/set_voxel_size.ijm
similarity index 100%
rename from registration/9.9.9/scripts/registration_targets/set_voxel_size.ijm
rename to registration/deprecated/scripts/registration_targets/set_voxel_size.ijm
diff --git a/registration/9.9.9/scripts/registration_targets/stomach_registration_targets.py b/registration/deprecated/scripts/registration_targets/stomach_registration_targets.py
similarity index 100%
rename from registration/9.9.9/scripts/registration_targets/stomach_registration_targets.py
rename to registration/deprecated/scripts/registration_targets/stomach_registration_targets.py
diff --git a/registration/9.9.9/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.ijm b/registration/deprecated/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.ijm
similarity index 100%
rename from registration/9.9.9/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.ijm
rename to registration/deprecated/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.ijm
diff --git a/registration/9.9.9/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.sh b/registration/deprecated/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.sh
similarity index 100%
rename from registration/9.9.9/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.sh
rename to registration/deprecated/scripts/transfer_ProSPr_data/ProSPr_copy_and_mirror.sh
diff --git a/registration/9.9.9/transformations/TransformParameters.BSpline10.9.9.9.txt b/registration/deprecated/transformations/TransformParameters.BSpline10.9.9.9.txt
similarity index 100%
rename from registration/9.9.9/transformations/TransformParameters.BSpline10.9.9.9.txt
rename to registration/deprecated/transformations/TransformParameters.BSpline10.9.9.9.txt
diff --git a/registration/9.9.9/transformations/TransformParameters.BSpline100.9.9.9.txt b/registration/deprecated/transformations/TransformParameters.BSpline100.9.9.9.txt
similarity index 100%
rename from registration/9.9.9/transformations/TransformParameters.BSpline100.9.9.9.txt
rename to registration/deprecated/transformations/TransformParameters.BSpline100.9.9.9.txt
diff --git a/registration/9.9.9/transformations/TransformParameters.BSpline30.9.9.9.txt b/registration/deprecated/transformations/TransformParameters.BSpline30.9.9.9.txt
similarity index 100%
rename from registration/9.9.9/transformations/TransformParameters.BSpline30.9.9.9.txt
rename to registration/deprecated/transformations/TransformParameters.BSpline30.9.9.9.txt
diff --git a/registration/9.9.9/transformations/TransformParameters.RotationPreAlign.0.0.0.txt b/registration/deprecated/transformations/TransformParameters.RotationPreAlign.0.0.0.txt
similarity index 100%
rename from registration/9.9.9/transformations/TransformParameters.RotationPreAlign.0.0.0.txt
rename to registration/deprecated/transformations/TransformParameters.RotationPreAlign.0.0.0.txt
diff --git a/registration/9.9.9/transformations/TransformParameters.Similarity.0.0.0.txt b/registration/deprecated/transformations/TransformParameters.Similarity.0.0.0.txt
similarity index 100%
rename from registration/9.9.9/transformations/TransformParameters.Similarity.0.0.0.txt
rename to registration/deprecated/transformations/TransformParameters.Similarity.0.0.0.txt
diff --git a/registration/9.9.9/transformations/TransformParameters.Similarity.0.txt b/registration/deprecated/transformations/TransformParameters.Similarity.0.txt
similarity index 100%
rename from registration/9.9.9/transformations/TransformParameters.Similarity.0.txt
rename to registration/deprecated/transformations/TransformParameters.Similarity.0.txt
diff --git a/registration/9.9.9/transformations/TransformParameters.Similarity.9.9.9.txt b/registration/deprecated/transformations/TransformParameters.Similarity.9.9.9.txt
similarity index 100%
rename from registration/9.9.9/transformations/TransformParameters.Similarity.9.9.9.txt
rename to registration/deprecated/transformations/TransformParameters.Similarity.9.9.9.txt