Deformation field versions

We have two different versions of bridging transforms available for download. Initial transforms were computed at high resolution using ANTs, but these are large enough to be impractical for distribution. Transforms at the highest resolution are available upon request.

Nifti (nii) transforms - Aug 2018

Our initial transforms were downsampled to a resolution of 0.88um isotropic, using this script.

H5 transforms - Feb 2019

We generated a new set of transformations using our hdf5 format for transformations. These store quantized versions (to sighed shorts) of the full-resolution deformation field. These are more similar to the original field than the downsampled fields we originally posted (difference guaranteed to be less than 0.04um). We also include quantized fields downsampled by factors of two and four.

Experiments

We converted deformation fields generated by ants to our hdf5 format quantized at signed shorts. Quantization was performed to limit errors to one-tenth of a pixel width (~0.044um) We also downsampled the field by factors of 2 and 4 in all dimensions. For each of these fields, we computed the difference of displacement vectors at many (~216k) points uniformly sampled over the field of view. This analysis was done for both forward and inverse deformation fields and six different transformations are tabulated below

Brief conclusions

1. Quantization works as advertized - max errors are always less than the error specified.
2. The errors incurred by downsampling vary quite a bit between different transformations (smoother transforms will incur less error).

Results

All errors reported are in units of microns.

Target template	Source template	Downsample factor	Direction	mean	median	max
JRC2018F	FCWB	1	inv	0.006438	0.002761	0.036021
			fwd	0.010671	0.010094	0.032244
		2	inv	0.010077	0.003238	0.282264
			fwd	0.015452	0.012649	0.318102
		4	inv	0.028926	0.004059	1.109862
			fwd	0.041967	0.019250	0.914898
	JFRC2010	1	inv	0.011600	0.011190	0.035953
			fwd	0.013564	0.013024	0.041042
		2	inv	0.019622	0.016937	0.243509
			fwd	0.022493	0.018962	0.269330
		4	inv	0.062983	0.049199	0.840153
			fwd	0.071045	0.052998	1.088046
	JFRC2013	1	inv	0.010517	0.010522	0.037791
			fwd	0.011967	0.011494	0.037541
		2	inv	0.015921	0.013978	0.313879
			fwd	0.016959	0.014803	0.201816
		4	inv	0.045357	0.028898	0.860191
			fwd	0.046943	0.032022	0.751963
JRC2018U	JFRC2010	1	inv	0.011587	0.011152	0.035081
			fwd	0.013412	0.012913	0.042212
		2	inv	0.019891	0.017134	0.314212
			fwd	0.022410	0.018926	0.292309
		4	inv	0.063698	0.049757	0.759477
			fwd	0.070460	0.052502	0.949169
	JFRC2013	1	inv	0.010220	0.010311	0.035432
			fwd	0.011869	0.011427	0.037649
		2	inv	0.015112	0.013440	0.282079
			fwd	0.016434	0.014465	0.204005
		4	inv	0.042249	0.026443	0.887520
			fwd	0.044366	0.029888	0.685095
	JRC2018F	1	inv	0.013220	0.013031	0.036252
			fwd	0.013277	0.013088	0.037465
		2	inv	0.013677	0.013080	0.128130
			fwd	0.013598	0.013028	0.098704
		4	inv	0.027382	0.020838	0.555527
			fwd	0.027301	0.020620	0.400653