chore: Add changelog for 0.16.4 (#1321)

## Summary by Sourcery

Document changes in version 0.16.4 including new features, bug fixes,
test dependency updates, CI/tooling enhancements, and security-related
dependency bumps.

New Features:
- Set units for viewer spawned from the view menu
- Add saving color maps in SOME tiffs

Bug Fixes:
- Fit ROI shape to image to fix data saving in batch processes
- Save selected directory in history when using the save dialog
- Stop using deprecated sentry_sdk method to fix --pre test
- Fix batch saving for mask segmentation projects
- Clean elements outside mask in multiple Otsu method

CI:
- Use the most recent macOS images on GitHub Actions

Tests:
- Upgrade constraint versions for various Python and testing
dependencies

Chores:
- Update pre-commit hooks, code formatting checks, licensing metadata,
and test log formatting
- Add review wait time and Dependabot cooldown in CI configuration

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

* **New Features**
  * Set units for viewers opened from the View menu.
  * Save color maps in compatible TIFF files.

* **Bug Fixes**
  * Improved ROI shape fitting during batch save.
  * Save directory history now persists reliably.
  * Enhanced batch save for mask segmentation projects.
  * Cleaned elements outside masks for multi-otsu workflows.

* **Documentation**
  * Added changelog entry for version 0.16.4.

* **Tests**
  * Consolidated automatic test/dependency upgrades.

* **Chores**
  * Routine maintenance, formatting, and CI/workflow updates.

* **Security**
  * Dependency updates within CI pipelines.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Author: Czaki

changelog.md

@@ -2,6 +2,57 @@
 
 All notable changes to this project will be documented in this file.
 
+## 0.16.4 - 2025-10-15
+
+### 🚀 Features
+
+- Set units for viewer spawned from the view menu ([#1308](https://github.com/4DNucleome/PartSeg/pull/1308))
+- Add saving color maps in OME tiffs ([#1312](https://github.com/4DNucleome/PartSeg/pull/1312))
+
+### 🐛 Bug Fixes
+
+- Fit ROI shape to image to solve problem of saving data in batch process ([#1288](https://github.com/4DNucleome/PartSeg/pull/1288))
+- If save dialog is used to select directory save it in history not parent ([#1289](https://github.com/4DNucleome/PartSeg/pull/1289))
+- Fix `--pre` test by stopping using the deprecated `sentry_sdk` method ([#1304](https://github.com/4DNucleome/PartSeg/pull/1304))
+- Fix saving in batch if the data is mask segmentation project ([#1309](https://github.com/4DNucleome/PartSeg/pull/1309))
+- Clean elements outside mask for multiple otsu method ([#1319](https://github.com/4DNucleome/PartSeg/pull/1319))
+
+### 🧪 Testing
+
+- [Automatic] Constraints upgrades: `pandas` ([#1285](https://github.com/4DNucleome/PartSeg/pull/1285))
+- [Automatic] Constraints upgrades: `ipykernel`, `numpy`, `scipy`, `sentry-sdk` ([#1287](https://github.com/4DNucleome/PartSeg/pull/1287))
+- [Automatic] Constraints upgrades: `imagecodecs`, `ipykernel`, `napari`, `sentry-sdk` ([#1290](https://github.com/4DNucleome/PartSeg/pull/1290))
+- [Automatic] Constraints upgrades: `napari`, `psygnal`, `sentry-sdk`, `superqt` ([#1295](https://github.com/4DNucleome/PartSeg/pull/1295))
+- [Automatic] Constraints upgrades: `pandas`, `requests` ([#1297](https://github.com/4DNucleome/PartSeg/pull/1297))
+- [Automatic] Constraints upgrades: `ipython`, `numpy`, `pydantic`, `qtconsole`, `scipy`, `sentry-sdk`, `tifffile`, `xlsxwriter` ([#1301](https://github.com/4DNucleome/PartSeg/pull/1301))
+- [Automatic] Constraints upgrades: `partsegcore-compiled-backend`, `psygnal`, `sentry-sdk` ([#1305](https://github.com/4DNucleome/PartSeg/pull/1305))
+- [Automatic] Constraints upgrades: `ipython`, `napari`, `pandas`, `pydantic`, `tifffile` ([#1311](https://github.com/4DNucleome/PartSeg/pull/1311))
+- [Automatic] Constraints upgrades: `pydantic`, `sentry-sdk` ([#1316](https://github.com/4DNucleome/PartSeg/pull/1316))
+
+### ⚙️ Miscellaneous Tasks
+
+- [pre-commit.ci] pre-commit autoupdate ([#1286](https://github.com/4DNucleome/PartSeg/pull/1286))
+- [pre-commit.ci] pre-commit autoupdate ([#1291](https://github.com/4DNucleome/PartSeg/pull/1291))
+- [pre-commit.ci] pre-commit autoupdate ([#1296](https://github.com/4DNucleome/PartSeg/pull/1296))
+- [pre-commit.ci] pre-commit autoupdate ([#1298](https://github.com/4DNucleome/PartSeg/pull/1298))
+- Add more wait on coderabbit review ([#1300](https://github.com/4DNucleome/PartSeg/pull/1300))
+- Use prek for initial check of code format ([#1299](https://github.com/4DNucleome/PartSeg/pull/1299))
+- [pre-commit.ci] pre-commit autoupdate ([#1302](https://github.com/4DNucleome/PartSeg/pull/1302))
+- Use most recent macOS images on GitHub Actions ([#1310](https://github.com/4DNucleome/PartSeg/pull/1310))
+- [pre-commit.ci] pre-commit autoupdate ([#1306](https://github.com/4DNucleome/PartSeg/pull/1306))
+- [pre-commit.ci] pre-commit autoupdate ([#1313](https://github.com/4DNucleome/PartSeg/pull/1313))
+- Add cooldown of dependabot PR ([#1317](https://github.com/4DNucleome/PartSeg/pull/1317))
+- Update licensing metadata to follow modern standards ([#1314](https://github.com/4DNucleome/PartSeg/pull/1314))
+- Make test log more readable by using 120 columns and colors ([#1320](https://github.com/4DNucleome/PartSeg/pull/1320))
+- [pre-commit.ci] pre-commit autoupdate ([#1318](https://github.com/4DNucleome/PartSeg/pull/1318))
+
+### 🛡️ Security
+
+- *(deps)* Bump actions/download-artifact from 4 to 5 in the github-actions group ([#1292](https://github.com/4DNucleome/PartSeg/pull/1292))
+- *(deps)* Bump pyvista/setup-headless-display-action from 3 to 4 ([#1294](https://github.com/4DNucleome/PartSeg/pull/1294))
+- *(deps)* Bump actions/checkout from 4 to 5 in the github-actions group ([#1293](https://github.com/4DNucleome/PartSeg/pull/1293))
+- *(deps)* Bump actions/setup-python from 5 to 6 in the github-actions group ([#1303](https://github.com/4DNucleome/PartSeg/pull/1303))
+
 ## 0.16.3 - 2025-07-10
 
 ### 🐛 Bug Fixes