Nutil - Neuroimaging utilities Releases

nutil 8.0.1 Macos M1 ARM

leuat@stage.nitrcce.org (Nicolaas Groeneboom) — Mon, 23 Jan 2023 16:08:00 GMT

M1 ARM version of Nutil. Initial version might have some bugs, please report them

nutil Nutil v0.8.0

sharoncy@stage.nitrcce.org (Sharon Christine Yates) — Fri, 01 Jul 2022 7:39:00 GMT

This is a major release with several new features. This includes:

• Point clouds that reflect the nonlinear refinement applied with the VisuAlign software.
• Updated object reports.
• Support for automatic generation of plots using Python scripts. These display the regional loads from the Reference Atlas reports and the Custom Region reports.
• Support for hierarchy.txt files from QCAlign to define the Custom Regions.
• Stop button in Nutil has been fixed.
• Improvements to error and warning messages.
• Updates to the help text in the Nutil GUI.

nutil Nutil v0.7.0

sharoncy@stage.nitrcce.org (Sharon Christine Yates) — Mon, 11 Oct 2021 6:47:00 GMT

Nutil v0.7.0[list][*]This release introduces a new reference atlas: the Waxholm Space Atlas of the Sprague Dawley rat v4 (WHSv4). The citation policy has been updated in the Nutil GUI and Nutil readthedoc for use of the Waxholm Space Atlas.[/list][list][*]The default customised regions for the WHSv3 have been updated. See the customised region.xlsx in the Nutil package for more information.[/list][list][*]Bug 1 that was discovered in Nutil v0.5.0 and partially fixed in v0.6.0 has been fully fixed in this version: the regional load outputs in the slice reports are now correct irrespective of the pixel scale.[/list][list][*]The user documentation has been considerably improved. All user manuals have been removed from the Nutil package, and replaced with a "user documentation" button in the Nutil GUI with a direct link to the Nutil readthedocs. These are updated on a regular basis, and also include user documentation for use of ilastik for the QUINT workflow.[/list][list][*]Improvements to error and warning messaging, and updates to the help text in the Nutil GUI.[/list]

nutil Nutil v0.6.0

sharoncy@stage.nitrcce.org (Sharon Christine Yates) — Fri, 26 Feb 2021 11:25:00 GMT

This release does not introduce new features but fixes recently discovered bugs affecting the Quantifier reports in some older versions of Nutil:

Bug 1: Regional load output in the slice reports are incorrect for Nutil v0.4.0 – v0.5.0. The other results in the reports are correct.

Bug 2: When using the mask feature: region pixels, region areas and loads in the reports are incorrect for Nutil v0.4.3 – v0.5.0. This bug does not affect analyses run without masks.

As the bugs affected core Quantifier functionality, we have introduced more stringent quality assurance routines, with continuous integration and automatic validation based on an expanded collection of ground truth datasets. We will provide more information about this in a future release.

nutil Nutil v 0.5.0

sharoncy@stage.nitrcce.org (Sharon Christine Yates) — Fri, 12 Feb 2021 12:56:00 GMT

Nutil version 0.407 included an upgrade to Qt 6. This introduced several major bugs due to Qt library updates. We have decided to delete this version entirely, and present Nutil v0.5.0 with upgrades and bug fixes to solve the issues found in Nutil v0.407:

- Upper size limit for the "segmentation" input files has been removed.
- TiffCreator library fix.
- Improved XML error messaging to prevent spontaneous crashes.
- QuickNII and VisuAlign user manuals have been added to the Nutil package.

The release notes that followed version 0.407 still apply:

There is a focus on usability improvements in the new release. This includes a scroll bar fix, improvements to file navigation, and improved error messaging. There are also several transform bug fixes.
Support has been implemented in Quantifier for JSON files containing the anchoring information. Either the XML or JSON file from QuickNII, or the JSON file from VisuAlign may now be used to supply the linear anchoring information needed for coordinate extraction. Support has also been implemented for navigation to masks from a separate folder, and not from the segmentation folder as in earlier versions.
There have been updates to the text in the Nutil GUI, and an extensive user manual update.

nutil Nutil v404

sharoncy@stage.nitrcce.org (Sharon Christine Yates) — Fri, 02 Oct 2020 11:48:00 GMT

Several new features have been implemented. Quantifier now assigns unique IDs to each object in the output images and reports allowing identification of individual object features. There is also the option to use your own reference atlas. TiffCreator now supports regular TIFF images enabling convertion to the tiled TIFF format that is compatible with the Transform feature. Several bug fixes and improvements to the inbuilt help text. User manuals have been updated.

nutil Nutil 0.403

sharoncy@stage.nitrcce.org (Sharon Christine Yates) — Fri, 19 Jun 2020 12:25:00 GMT

Significant improvements to the Quantifier reports including a bug fix for region area quantifications (the previous version had a slight rounding up error; old reports are still useable, but we recommend switching to the latest version). The Transform feature now supports import of file names and transformation parameters from an Excel template titled "TransformTemplate" (included in the Nutil package). Improvements to the inbuilt help text throughout. User manual updates.

nutil Nutil 0.402

sharoncy@stage.nitrcce.org (Sharon Christine Yates) — Sun, 05 Apr 2020 17:43:00 GMT

Several bug fixes including a major fix for Nutil Quantifier analysis with WHS rat atlas v3. Updated Nutil user manual and new ilastik user manual.

nutil Nutil 0.4.01

sharoncy@stage.nitrcce.org (Sharon Christine Yates) — Fri, 14 Feb 2020 11:53:00 GMT

Two minor bug fixes and command line interface script for batch processing added.

nutil Nutil 0.4

sharoncy@stage.nitrcce.org (Sharon Christine Yates) — Fri, 31 Jan 2020 12:59:00 GMT

Nutil v0.4.

Major release with new GUI. Bug fixes and performance improvements. Improved error messaging. Detailed help text for every input parameter. New resize feature implemented. Command line version.