Release notes

1.1.0 (7 March 2023)

New features

  • Add a –compresslevel option for controlling the GZip compression level. Many thanks to Bradley Lowekamp for implementing this feature in PR #24 / PR #26.

  • Add the –type and –encoding options to the all-in-one volume-to-precomputed-pyramid script. Many thanks to Xiao Gui for implementing this feature in PR #29.

Python version support

  • Add support and tests for Python 3.11.

Bug fixes

  • Fix volume reading with recent Nibabel >= 5.0.0, due to the expired deprecation of get_data. Many thanks to Bradley Lowekamp for reporting this bug, and to Xiao Gui for implementing the fix in PR #28.

1.0.0 (17 November 2021)

New features

  • Support for RGB NIfTI. Many thanks to Xiao Gui for implementing this feature in PR #15.

  • Support for LZW-compressed TIFF files. Many thanks to Xiao Gui for implementing this feature in PR #14.

Python version support

  • Add support and tests for Python 3.8, 3.9, and 3.10.

  • Drop support for Python 3.4

Bug fixes

  • Fix mesh conversion with recent versions of Nibabel (commit c03bb5c8).

  • Bump the minimum version of tqdm to prevent a blocking crash (see tqdm bug#613).

0.3.0 (28 November 2018)

Bug fixes

  • Fix the swarm of warning messages that appear when downscaling images of integer type by the averaging method.

Other improvements

  • The default downscaling method is now chosen automatically based on the type of dataset: image uses local averaging, segmentation uses striding.

  • The command-line interface of mesh-to-precomputed was changed to work with Accessors, instead of being restricted to files. The command also now reads and writes the info file to make sure that Neuroglancer knows where to find the mesh fragments.

  • Introduced a new command link-mesh-fragments to create the small JSON files that are required to link segmentation labels to mesh fragments.

0.2.0 (16 October 2018)

Changes that affect converted data

  • Use correct rounding when downscaling by local average (commit 8f77b486).

Bug fixes

  • Fixed passing of options between functions (issue #7, commit 67430f13, commit f0e1e79d). Thanks to Ben Falk for reporting and fixing the issue.

  • Fixed the conversion of stacks of multi-channel images (commit ff8d4dcc).

  • Fixed a crash when flippping mesh triangles for negative-determinant transformations (commit 97545914, issue #5).

  • Fixed a bug where the chunk size of extremely anisotropic volumes was set to zero (commit 92264c91).

  • Fixed loading of uint64 TIFF files (issue #8). Thanks to Ben Falk for reporting and fixing the issue.

Other improvements

  • Introduced a new command volume-to-precomputed-pyramid for all-in-one conversion of volume in simple cases.

  • Introduced a new command convert-chunks which can be used to convert existing data in Neuroglancer prec-computed format to a different encoding.

  • slice-to-precomputed now uses proper rounding and clamping for performing data-type conversion.

  • Improved the conversion of meshes to Neuroglancer-compatible VTK format, and got rid of the dependency on PyVTK.

  • Improved the performance of common use-cases by loading the full volume in memory by default. The old behaviour can be restored with --mmap.

0.1.0 (7 February 2018)

Initial PyPI release.