dvp-io - v0.3.0

Version 0.3.0

First external contribution by @AntonSchuele!

Features 🚀

• CZI scene support by @AntonSchuele and @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/115

API change ⚠️

This introduces the new scene argument in the read_czi function (backwards compatible, defaults to all scenes)

Docs 📄

• [Doc] Update installation instructions to account for pypi release by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/112
• [Doc] Improved docstring for read_czi function by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/115

Automated 🤖

• [VERSION] Bump version to 0.3.0 by @github-actions[bot] in https://github.com/lucas-diedrich/dvp-io/pull/116

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Full Changelog: https://github.com/lucas-diedrich/dvp-io/compare/v0.2.2...v0.3.0

- Python
Published by lucas-diedrich 11 months ago

dvp-io - v0.2.2

🎉 First pypi release

What's Changed

Removed alphabase development dependency

Full Changelog

https://github.com/lucas-diedrich/dvp-io/compare/v0.2.1...v0.2.2

Remove dependency

• [Dep] Update dependencies by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/103
• Bump version v0.2.1dev-1 by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/106
• AnnData factory by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/107
• Remove alphabase dev dependency by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/111

Release

• [Release] Manually bump version by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/102
• [Release] Bump version to 0.2.2 by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/110

- Python
Published by lucas-diedrich about 1 year ago

dvp-io - v0.2.1

This release includes bug fixes and extended functionality in the dvpio.read.shapes.read_lmd function.

🚀 New features

read_lmd: Select the type of transformation when aligning lmd shapes and calibration points (affine/similarity/rigid transform).

🚨 Breaking changes

Added arguments in the dvpio.read.shapes.read_lmd function (precision, transformation_type). Changed default behavior of the function (before: precision=3, transformation_type="affine", now: precision=6, transformation_type="similarity"

🛠️ Bug fixes

• Increased accuracy in the affine transformation of the dvpio.read.shapes.read_lmd function (before: 3 digit precision, now per default 6) to mitigate small errors in the transformation
• Openslide reader: Fixed bug in dvpio.read.images.openslide that made the image import fail and added relevant test cases.

📖 Documentation

• Updated tutorial 004 (Real-world example - Analysis of scDVP liver zonation dataset
• Updated installation instructions to account for potentially missing libssh2 C++ dependency.

What's Changed

• [VERSION] Bump version to 0.1.1-dev0 (merge after release) by @github-actions in https://github.com/lucas-diedrich/dvp-io/pull/93
• [Documentation] Update installation instructions by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/96
• [Bugfix] Transformation | Similarity transformation by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/97
• [VERSION] Bump version to 0.2.0 by @github-actions in https://github.com/lucas-diedrich/dvp-io/pull/98
• [Bugfix] Fix docs by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/100
• [Bugfix] Fix openslide reader by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/101

Full Changelog: https://github.com/lucas-diedrich/dvp-io/compare/v0.1.1...v0.2.1

- Python
Published by lucas-diedrich about 1 year ago

dvp-io - v.0.1.1

Stability improvements.

What's Changed

• Improve installation instructions by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/86
• [Hotfix] Fix alphabase dependency by explicitly setting commit hash in pyproject.toml by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/87
• [Bump version] 0.1.0-dev0 by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/91
• [VERSION] Bump version to 0.1.0 by @github-actions in https://github.com/lucas-diedrich/dvp-io/pull/92

Full Changelog: https://github.com/lucas-diedrich/dvp-io/compare/v0.1.0...v0.1.1

- Python
Published by lucas-diedrich over 1 year ago

dvp-io - 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 https://github.com/lucas-diedrich/dvp-io/pull/69 * Refactor patching algorithm by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/71 * Metadata reader openslide by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/73 * Metadata parser by @lucas-diedrich in https://github.com/lucas-diedrich/dvp-io/pull/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 https://github.com/lucas-diedrich/dvp-io/pull/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 https://github.com/lucas-diedrich/dvp-io/pull/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 https://github.com/lucas-diedrich/dvp-io/pull/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 https://github.com/lucas-diedrich/dvp-io/pull/67

Misc

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

Full Changelog: https://github.com/lucas-diedrich/dvp-io/compare/v0.0.2...v0.1.0

- Python
Published by lucas-diedrich over 1 year ago

dvp-io - v0.0.2

Bug fixes

• Bug fixes for read_czi function for Gray8 pixel type. The function assumed a bitrange of 28 which is not necessarily given for this pixel type. Extended range to 216.

Tutorials

• Tutorial on downstream analysis of spatialdata with scPortrait
• Tutorial on downstream analysis of spatialdata with sopa

- Python
Published by lucas-diedrich over 1 year ago

dvp-io - v0.0.1

Initial support for images, shapes, and proteomics data.

Images

Supported formats include .tiff (fluorescence channels), .czi (fluorescence/brightfield), and openslide compatible brightfield images (e.g. mirax)

Shapes

Read and write functionalities for LMD-compatible .xml files.

Proteomics data

Support for DIANN reports, alphaDIA reports, and others (see alphabase).

Tutorials

Initial tutorials on plotting and interactive exploration with napari for mock and real-world data.

- Python
Published by lucas-diedrich over 1 year ago