Magellanmapper

- Fixed `setup.py` to include PyYAML (dependency introduced in MagellanMapper v1.2.1)

Server dependency Changes

- `Dockerfile`s are included, with one version based on Miniconda3 and another on Ubuntu 18.04

Highlights in v1.6 pre-releases

- Smoother, faster interactions with main plots, including atlas label name display, label editing, and pan and zoom navigation
- Available as binary wheel to install without requiring the source code
- Faster, lighter installation with fewer required dependency packages
- Extends suppor to Python 3.11 and defaults to Python 3.9
- Simpler entry point to launch MagellanMapper: `mm`
- Supports ITK-Elastix for image registration
- Atlases can be downloaded directly through [`BrainGlobe`](https://github.com/brainglobe/bg-atlasapi) (see the new "Atlases" panel)
- Atlas regions can be searched (see "Atlases > Region")
- Atlas Editor planes can be reordered or turned off
- Detection channels can be selected independently of the loaded image to overlay prior detections or compare channels (see "Detect > Chl")
- Images can be viewed as RGB (see "ROI > Channels") or merged channels
- [Jupyter Notebook tutorial](https://github.com/sanderslab/magellanmapper/blob/master/bin/sample_cmds_bash.ipynb) for running common tasks
- Fixed installation on Apple Silicon (Mac M-chip) platforms

Major changes since beta 3

- Fixed installation on Apple Silicon (Mac M-chip) platforms (634)
- Select colormaps for each channel (574)
- Fixed image adjustment controls
- Fixed synchronization between images and adjustment controls (576)
- Fixed intensity sliders to cover the full range (572, 576, 606, 613)
- Fixed intensity range of "filtered" ROI and overview images (613)

See the [full release notes draft here](https://github.com/sanderslab/magellanmapper/blob/v1.6b4/docs/release/release_v1.6.md) for more details.

All Changes
<details>
<summary>Show details</summary>

* Bump default Python version to v3.9 by yoda-vid in https://github.com/sanderslab/magellanmapper/pull/559
* Bump imageio from 2.31.3 to 2.31.4 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/560
* Bump tifffile from 2023.9.18 to 2023.9.26 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/561
* Bump scipy from 1.11.2 to 1.11.3 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/562
* Fix ReadTheDocs for Python 3.9 by yoda-vid in https://github.com/sanderslab/magellanmapper/pull/563
* Bump cycler from 0.11.0 to 0.12.0 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/564
* Bump imageio from 2.31.4 to 2.31.5 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/565
* Bump fonttools from 4.42.1 to 4.43.0 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/566
* Bump charset-normalizer from 3.2.0 to 3.3.0 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/568
* Bump urllib3 from 2.0.5 to 2.0.6 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/569
* Bump rich from 13.5.3 to 13.6.0 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/570
* Bump packaging from 23.1 to 23.2 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/571
* Bump scikit-image from 0.21.0 to 0.22.0 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/573
* Extend image adjustment sliders to use full intensity range by yoda-vid in https://github.com/sanderslab/magellanmapper/pull/572
* Store the last opened image via the GUI in preferences by yoda-vid in https://github.com/sanderslab/magellanmapper/pull/575
* Select colormaps in the GUI by yoda-vid in https://github.com/sanderslab/magellanmapper/pull/574
* Fix restoring intensity when showing a multi-channel image with deselected channels by yoda-vid in https://github.com/sanderslab/magellanmapper/pull/576
* Bump cycler from 0.12.0 to 0.12.1 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/577
* Bump fonttools from 4.43.0 to 4.43.1 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/578
* Bump traits from 6.4.2 to 6.4.3 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/579
* Bump urllib3 from 2.0.6 to 2.0.7 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/581
* Bump pyqt5-sip from 12.12.2 to 12.13.0 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/582
* Bump imageio from 2.31.5 to 2.31.6 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/583
* Bump charset-normalizer from 3.3.0 to 3.3.1 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/584
* Bump numpy from 1.26.0 to 1.26.1 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/586
* Bump networkx from 3.1 to 3.2 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/587
* Bump pandas from 2.1.1 to 2.1.2 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/588
* Bump networkx from 3.2 to 3.2.1 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/589
* Bump pyqt5 from 5.15.9 to 5.15.10 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/590
* Bump charset-normalizer from 3.3.1 to 3.3.2 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/591
* Bump contourpy from 1.1.1 to 1.2.0 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/593
* Bump matplotlib from 3.8.0 to 3.8.1 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/594
* Bump importlib-resources from 6.1.0 to 6.1.1 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/596
* Bump imageio from 2.31.6 to 2.32.0 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/597
* Bump fonttools from 4.43.1 to 4.44.3 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/598
* Fix making density images with ITK by yoda-vid in https://github.com/sanderslab/magellanmapper/pull/599
* Support generating regional heat maps from the volume metrics output by yoda-vid in https://github.com/sanderslab/magellanmapper/pull/600
* Remove `verify_tol_factor` from identical block settings check by yoda-vid in https://github.com/sanderslab/magellanmapper/pull/603
* Exclude negative intensities by default in image sliders by yoda-vid in https://github.com/sanderslab/magellanmapper/pull/606
* Workaround Matplotlib error when turning off alpha blending by yoda-vid in https://github.com/sanderslab/magellanmapper/pull/607
* Fix exporting multiple planes from single image by yoda-vid in https://github.com/sanderslab/magellanmapper/pull/611
* Bump certifi from 2023.7.22 to 2023.11.17 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/602
* Bump imageio from 2.32.0 to 2.33.1 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/608
* Bump pillow from 10.0.1 to 10.2.0 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/610
* Round-up of 2D plot fixes by yoda-vid in https://github.com/sanderslab/magellanmapper/pull/612
* Fix running Mayavi on Windows by yoda-vid in https://github.com/sanderslab/magellanmapper/pull/618
* Bump rich from 13.6.0 to 13.7.0 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/614
* Bump scipy from 1.11.3 to 1.12.0 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/615
* Bump matplotlib from 3.8.1 to 3.8.2 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/616
* Restore image settings during refresh by yoda-vid in https://github.com/sanderslab/magellanmapper/pull/613
* Bump pywavelets from 1.4.1 to 1.5.0 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/619
* Bump idna from 3.4 to 3.6 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/620
* Bump pandas from 2.1.2 to 2.2.0 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/621
* Fix ROI Editor margin and plane number by yoda-vid in https://github.com/sanderslab/magellanmapper/pull/622
* Bump tzdata from 2023.3 to 2024.1 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/623
* Bump pygments from 2.16.1 to 2.17.2 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/624
* Bump importlib-metadata from 6.8.0 to 7.1.0 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/628
* Bump pillow from 10.2.0 to 10.3.0 in /envs by dependabot in https://github.com/sanderslab/magellanmapper/pull/629
* Workaround for Apple Silicon platforms by yoda-vid in https://github.com/sanderslab/magellanmapper/pull/634


**Full Changelog**: https://github.com/sanderslab/magellanmapper/compare/v.1.6b3...v1.6b4
</details>

Highlights in v1.6 pre-releases

- Smoother, faster interactions with main plots, including atlas label name display, label editing, and pan and zoom navigation
- Available as binary wheel to install without requiring the source code
- Faster, lighter installation with fewer required dependency packages
- Extends support to Python 3.11 and updates default to Python 3.9
- Simpler entry point to launch MagellanMapper: `mm`
- Supports ITK-Elastix for image registration
- Atlases can be downloaded directly through [`BrainGlobe`](https://github.com/brainglobe/bg-atlasapi) (see the new "Atlases" panel)
- Atlas regions can be searched (see "Atlases > Region")
- Atlas Editor planes can be reordered or turned off
- Detection channels can be selected independently of the loaded image to overlay prior detections or compare channels (see "Detect > Chl")
- Images can be viewed as RGB (see "ROI > Channels") or merged channels
- [Jupyter Notebook tutorial](https://github.com/sanderslab/magellanmapper/blob/master/bin/sample_cmds_bash.ipynb) for running common tasks

Major changes since beta 2

- Fixed running on Python >= 3.9 (559)
- Fixed resetting label opacity when scrolling among planes (552)

See the [full release notes draft here](https://github.com/sanderslab/magellanmapper/blob/v1.6b3/docs/release/release_v1.6.md) for more details.

Highlights in v1.6 pre-releases

- Smoother, faster interactions with main plots, including atlas label name display, label editing, and pan and zoom navigation
- Available as binary wheel to install without requiring the source code
- Faster, lighter installation with fewer required dependency packages
- Extends suppor to Python 3.11
- Simpler entry point to launch MagellanMapper: `mm`
- Supports ITK-Elastix for image registration
- Atlases can be downloaded directly through [`BrainGlobe`](https://github.com/brainglobe/bg-atlasapi) (see the new "Atlases" panel)
- Atlas regions can be searched (see "Atlases > Region")
- Atlas Editor planes can be reordered or turned off
- Detection channels can be selected independently of the loaded image to overlay prior detections or compare channels (see "Detect > Chl")
- Images can be viewed as RGB (see "ROI > Channels") or merged channels
- [Jupyter Notebook tutorial](https://github.com/sanderslab/magellanmapper/blob/master/bin/sample_cmds_bash.ipynb) for running common tasks

Major changes since beta 1

- Python 3.10-3.11 are now supported (379, 517)
- Supports image I/O and registration through ITK-Elastix (495, 497, 500, 504)
- "Merge" option in the ROI panel to merge channels using additive blending (492)
- Use core fonts in PDF/PS file exports to keep vector text (486)
- Fixed parsing some metadata when importing files with Bio-Formats (502)

See the [full release notes draft here](https://github.com/sanderslab/magellanmapper/blob/v1.6b2/docs/release/release_v1.6.md) for more details.

Highlights in v1.6 pre-releases

- Smoother, faster interactions with main plots, including atlas label name display, label editing, and pan and zoom navigation
- Available as binary wheel to install without requiring the source code
- Simpler entry point to launch MagellanMapper: `mm`
- Atlases can be downloaded directly through [`BrainGlobe`](https://github.com/brainglobe/bg-atlasapi) (see the new "Atlases" panel)
- Atlas regions can be searched (see "Atlases > Region")
- Detection channels can be selected independently of the loaded image to overlay prior detections or compare channels (see "Detect > Chl")
- Images can be viewed as RGB (see "ROI > Channels")
- [Jupyter Notebook tutorial](https://github.com/sanderslab/magellanmapper/blob/master/bin/sample_cmds_bash.ipynb) for running common tasks

Major changes since alpha 3

- Mayavi/VTK are now optional, installed in the `3d` group (455)
- Basic spectral unmixing through channel subtraction (458)
- Fixed redundant triggers when adjusting the displayed image (474)
- Fixed conflict between shortcut to add blob and jumping to ROI plane (`ctrl+click`) by changing the jump shortcut to `j+click` (456)
- Fixed groupwise registration for current atlas profiles, turned off default cropping (444)
- More fixes to blob archives with custom columns (449, 475)
- 2D plots, R stats, and server pipeline improvements (445, 451, 457, 469, 470)

See the [full release notes draft here](https://github.com/sanderslab/magellanmapper/blob/49ff450f78477087807b282d4d9f43f8ba4c7bf4/docs/release/release_v1.6.md) for more details.

Highlights in v1.6 pre-releases

- Smoother, faster interactions with main plots, including atlas label name display, label editing, and pan and zoom navigation
- Available as binary wheel to install without requiring the source code
- Simpler entry point to launch MagellanMapper: `mm`
- Atlases can be downloaded directly through [`BrainGlobe`](https://github.com/brainglobe/bg-atlasapi) (see the new "Atlases" panel)
- Atlas regions can be searched (see "Atlases > Region")
- Detection channels can be selected independently of the loaded image to overlay prior detections or compare channels (see "Detect > Chl")
- Images can be viewed as RGB (see "ROI > Channels")
- [Jupyter Notebook tutorial](https://github.com/sanderslab/magellanmapper/blob/master/bin/sample_cmds_bash.ipynb) for running common tasks

Major changes since alpha 2

- Workaround for Qt run issue (431)

See the [full release notes draft here](https://github.com/sanderslab/magellanmapper/blob/af4d0c0700ffade7fe1cbc83c63c8583dc04d04e/docs/release/release_v1.6.md) for more details.