v0.1.0

Version 0.1.0 is out with many exciting features!

New features 🚀

Metadata parsers

DVP-IO is now able to automatically parse relevant metadata (resolution, objective magnification, channel names) from the provided microscopy files. This simplifies the usage and API of the read_czi function and enables users to extract more relevant data from the microscopy slides. Metadata reading capabilities are exposed with the new dvpio.read.image.read_metadata function.

Related PRs

• Metadata Parsing | CZI by @lucas-diedrich in #69
• Refactor patching algorithm by @lucas-diedrich in #71
• Metadata reader openslide by @lucas-diedrich in #73
• Metadata parser by @lucas-diedrich in #74

Release workflow

DVP-IO now has an automated release workflow that significantly facilitates versioning and thus improves reproducibility and bug-hunting.

Related PRs

• Release workflow by @lucas-diedrich in #75

Breaking changes 🚨

CZI reader

Per default, the CZI reader (dvpio.read.image.read_czi) now automatically extracts all channels (compared to previously only the first channel). While this is typically more convenient for users and covers most use cases, this might introduce unexpected behavior in previous workflows that explicitly only need to extract the first channel but do not explicitly pass the channel=0 argument to the function.

Related PRs

• Metadata Parsing | CZI by @lucas-diedrich in #69

Bug fixes 🛠️

CZI reader - BGR/RGB channels

Fixes severe bug in the CZI reader (dvpio.read.image.read_czi) that labels channels in CZI BGR images in the reversed order (i.e. uses RGB order instead of BGR order).

• [Refactor] Refactor patching algorithm and czi reader by @lucas-diedrich in #67

CZI reader - axes swapped

Fixes severe bug in the CZI reader (dvpio.read.image.read_czi) that lead to the x/y axes in images being swapped.

• [Refactor] Refactor patching algorithm and czi reader by @lucas-diedrich in #67

Misc

• [Docs] Change order of warning in docstrings by @lucas-diedrich in #66
• [Docs] Fix build by @lucas-diedrich in #68
• Release workflow by @lucas-diedrich in #75
• [Fix] Set current version correctly by @lucas-diedrich in #76
• Set dev version by @lucas-diedrich in #77
• [Fix] Rename to .bumpversion.toml by @lucas-diedrich in #78
• Delete bumpversion, rename to by @lucas-diedrich in #79
• [VERSION] Bump patch from 0.0.2 dev0 prepare next version by @lucas-diedrich in #82
• [VERSION] Bump version to 0.0.3-dev1 by @github-actions in #83
• [VERSION] Bump version to 0.1.0 by @github-actions in #84

Full Changelog: v0.0.2...v0.1.0