CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.9.2] - 2025-08-06

Added functionality and tests to subset to specific channels by indexing #36

Added functionality and tests to subset to specific image region #36

Added functionality to load data into memory-mapped array, that is stored under a path provided by the user (so it can manually be deleted afterwards) #36

Changed data_start_offset & data_end_offset conditions such that empty acquisitions are allowed (but warning printed) #37

[0.8.0] - 2024-09-06

Added the option to return raw data for read_slide, read_panorama, read_before_ablation_image, read_after_ablation_image functions.

Fixed a bug where the reading of ablation image functions was returning an extra byte at the end of the DotNet Binary Serialization Record.

[0.7.0] - 2023-08-11

Implemented checks for overlapping raw data blocks in MCD file metadata #6

Implemented lenient extraction of corrupted imaging data #19

[0.6.2] - 2023-01-31

Maintenance release

Made modules public

Renamed MCDFile.metadata to MCDFile.schema_xml

Toolchain (black, flake8, isort, mypy, pre-commit)

Updated GitHub Actions workflows

Small bugfixes and improvements

Python 3.11 compatibility

[0.6.1] - 2022-01-28

Rename MCDXMLParser to MCDParser

Refactor and simplify MCDParser usage

BREAKING CHANGES in MCDFile:

• Renamed MCDFile.metadata_xml_str to MCDFile.metadata
• Removed MCDFile.metadata_xml and MCDFile.metadata_xmlns (use MCDParser instead)

[0.6.0] - 2022-01-28

Expose MCDXMLParser

[0.5.0] - 2021-12-02

Refactored metadata accessors

Refactored accessors for ROI points/coordinates

Added link between acquisitions and associated panoramas

Renamed IMCMcdFile and IMCTxtFile to MCDFile and TXTFile

[0.4.2] - 2021-11-01

Use pandas for reading TXT files (better performance)

[0.4.1] - 2021-11-01

Added support for Python 3.10

[0.4.0] - 2021-10-19

Added support for older versions of the Fluidigm software

Use heuristics for determining acquisition start position

Add offline unit tests for data from (Damond et al., 2019)

Fix a numerical bug in determining panorama image dimensions

[0.3.1] - 2021-10-11

Renamed IMCMCDFile and IMCTXTFile to IMCMcdFile and IMCTxtFile, respectively

[0.3.0] - 2021-10-11

Retain meta-information after closing a file

Pre-compile regular expressions for faster parsing

Separately store and expose channel metals & masses; change channel name format from f"{metal}({mass})" to f"{metal}{mass}" for backwards compatibility with imctools

[0.2.0] - 2021-10-09

Use dataclasses instead of NamedTuples

Renamed TXTFile and MCDFile to IMCTXTFile and IMCMCDFile, respectively

IMCTXTFile and IMCMCDFile now implement a shared IMCFileBase interface

IMCTXTFile and Acquisition now implement a shared AcquisitionBase interface

[0.1.2] - 2021-10-09

Explicit acquisition image reconstruction based on pixel indices

[0.1.1] - 2021-10-09

Minor documentation changes

[0.1.0] - 2021-10-09

Initial release [0.7.0]: https://github.com/BodenmillerGroup/readimc/compare/v0.6.2...v0.7.0 [0.6.2]: https://github.com/BodenmillerGroup/readimc/compare/v0.6.1...v0.6.2 [0.6.1]: https://github.com/BodenmillerGroup/readimc/compare/v0.6.0...v0.6.1 [0.6.0]: https://github.com/BodenmillerGroup/readimc/compare/v0.5.0...v0.6.0 [0.5.0]: https://github.com/BodenmillerGroup/readimc/compare/v0.4.2...v0.5.0 [0.4.2]: https://github.com/BodenmillerGroup/readimc/compare/v0.4.1...v0.4.2 [0.4.1]: https://github.com/BodenmillerGroup/readimc/compare/v0.4.0...v0.4.1 [0.4.0]: https://github.com/BodenmillerGroup/readimc/compare/v0.3.1...v0.4.0 [0.3.1]: https://github.com/BodenmillerGroup/readimc/compare/v0.3.0...v0.3.1 [0.3.0]: https://github.com/BodenmillerGroup/readimc/compare/v0.2.0...v0.3.0 [0.2.0]: https://github.com/BodenmillerGroup/readimc/compare/v0.1.2...v0.2.0 [0.1.2]: https://github.com/BodenmillerGroup/readimc/compare/v0.1.1...v0.1.2 [0.1.1]: https://github.com/BodenmillerGroup/readimc/compare/v0.1.0...v0.1.1 [0.1.0]: https://github.com/BodenmillerGroup/readimc/releases/tag/v0.1.0