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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.

[0.16.3] - 2024-05-29

Changed

  • Updated readimc to 0.7.0

Added

  • Added the option for lenient parsing of corrupted ROIs

[0.16.2] - 2023-08-15

Changed

  • Enhanced error handling for missing ROIs #184

0.16.1 - 2023-05-07

Fixed

  • Broken external preprocessing for files with OME-suffix #181

0.16.0 - 2023-02-03

Added

  • New steinbock view command (napari) #27
  • New steinbock utils expand command (mask expansion) #106
  • New steinbock apps jupyter and steinbock apps jupyterlab commands
  • New steinbock -cellpose container flavor (cellpose segmentation) #118
  • New steinbock -xpra container flavor (web-based graphical user interfaces)
  • Preparations for tensorflow-enabled arm64-based linux base images #98
  • Added $RUN_FIXUID environment variable (prepare for Singularity) #156

Changed

  • Dependency upgrades
  • CellProfiler upgrade to 4.2.5
  • Harmonization of --unzip defaults (IMC preprocessing)
  • Separate virtual environments for steinbock and CellProfiler
  • Improved development environment (toolchain configuration, test skeletons)
  • Revised steinbock Docker container installation instructions #160

Fixed

  • Missing error message in measurement commands #151

0.15.0 - 2022-09-15

  • #136 Fix histoCAT mask export
  • #146 Fix relabeling during stitching
  • Upgrade deepcell 0.12.2 to 0.12.3
  • Upgrade CellProfiler 4.2.1 to 4.2.4
  • Upgrade other dependencies
  • #109 Support 2-6 channel TIFF files
  • #66 Include panel/image metadata in anndata exports
  • #117 Extract and process images from .zip archives file by file
  • #104 #121 Documentation improvements
  • #139 #140 #141 API improvements

0.14.2 - 2022-06-29

  • Upgrade DeepCell (to 0.12.2) and other dependencies
  • #132 Write images as ImageJ TIFF for supported data types only
  • #133 Exclude hidden files from processing

0.14.1 - 2022-06-08

  • #127 Fix CUDA build
  • #128 Fix steinbock wheel

0.14.0 - 2022-06-02

  • #111 Include package data in Python package
  • #122 Use logging instead of click.echo
  • #123 Custom exception handling
  • #124 Fix neighbor measurement
  • #125 Upgrade to DeepCell 0.12.0
  • Various minor bugfixes and improvements
  • Upgrade all dependencies

0.13.5 - 2022-02-21

  • Fix dependency version pinning

0.13.4 - 2022-02-09

  • Fix DeepCell YAML loading

0.13.3 - 2022-02-08

  • Fix ambiguous txt file matching (see #100)

0.13.2 - 2022-02-04

  • Maintenance release

0.13.1 - 2022-01-26

  • Fix GPU support

0.13.0 - 2022-01-26

  • Full memory mapping support
  • Fixed zero division error in deepcell normalization
  • Added GPU support (switched to Ubuntu 18.04-based tensorflow base image)
  • Fixed IMC panel preprocessing
  • Upgraded dependencies

0.12.0 - 2022-01-08

  • In-memory mosaics
  • Stabilized image/mask IO
  • Standardized command output
  • Minor changes, documentation

0.11.0 - 2021-12-28

  • Removed steinbock version check
  • Fix IMC panel preprocessing (channel order)
  • Make CLI usable when using PyPI package install
  • Renamed --mask and --probab parameters to --masks and --probabs, respectively
  • Clean histoCAT export file names
  • Required -o parameter for data export

0.10.7 - 2021-12-27

  • Fix IMC panel preprocessing

0.10.6 - 2021-12-27

  • Customizable IMC panel columns

0.10.5 - 2021-12-25

  • Fix IMC panel preprocessing

0.10.4 - 2021-12-25

  • Fix IMC panel preprocessing

0.10.3 - 2021-12-20

  • Fix memory issue with Ilastik image creation

0.10.2 - 2021-12-07

  • Fix deepcell incompatibility with scikit-image upgrade

0.10.1 - 2021-12-06

  • Fix AnnData export warning
  • Allow duplicated txt/mcd file names
  • Upgrade readimc and other dependencies

0.10.0 - 2021-11-05

  • Unified object data (csv, fcs, anndata) export commands
  • Improved anndata export: concatenation, intensities, graphs
  • Improved IMC panel preprocessing: support for different panels
  • Added functionality for importing image data using imageio
  • Clean up and upgrade dependencies, including deepcell 0.11.0
  • Change image file name pattern to make acquisitions sortable
  • Upgrade readimc for faster reading of .txt files
  • Change CellProfiler input image dtype to uint16
  • Change histoCAT mask dtype to uint16
  • Updated documentation on Docker

0.9.1 - 2021-10-12

  • Fixed preprocessing of IMC Segmentation Pipeline panels

0.9.0 - 2021-10-11

  • Upgraded dependencies
  • Improved documentation
  • Reduced Docker image size
  • Replaced imctools with readimc
  • Added dockerized unit tests (w.i.p.)
  • Restructured package, renamed tools to utils
  • Updated package information, added all extra
  • Added histoCAT image export command
  • Added steinbock logo (Nils Eling)

0.8.1 - 2021-09-22

  • Added missing deepcell column to IMC panel preprocessing from raw data

0.8.0 - 2021-09-21

  • Improved error handling & messages
  • Restructured & improved documentation
  • IMC preprocessing: extract image metadata
  • Fix steinbock versioning in docker container
  • Upgraded dependencies, including deepcell 0.10.0
  • Fix permission issues using fixuid approach

0.7.3 - 2021-09-09

  • Make container ready for passwd mounting
  • Fix OME export destination directory name

0.7.2 - 2021-09-09

  • Fixed graph export

0.7.1 - 2021-09-09

  • Renamed graph measurement to neighbor measurement

0.7.0 - 2021-09-01

  • Improved graph construction performance
  • Added new graph construction methods, including pixel expansion
  • Removed distance computation in favor of more performant graph construction
  • Fixed IMC panel preprocessing (unreported bugs)
  • Fixed Ilastik pixel classification (unreported bugs)

0.6.2 - 2021-08-21

  • Improved documentation & switched to versioned documentation
  • Improved IMC Segmentation Pipeline panel support (#38)

0.6.1 - 2021-08-17

  • Fixed data type conversion upon image loading

0.6.0 - 2021-08-17

  • Updated CellProfiler and other dependencies (#22)
  • Switch from Docker Hub to GitHub Container Registry (#34)
  • Various compatibility improvements and bugfixes (#21, #28, #32, #35)

0.5.6 - 2021-06-29

  • Switch to bilinear interpolation for Ilastik mean channel
  • Make image/mask data type configurable via environment variables

0.5.5 - 2021-06-28

  • Fix steinbock version check
  • Add meanfactor option to Ilastik (compatibility with IMC segmentation pipeline)
  • Save Ilastik images/crops as uint16 (compatibility with IMC segmentation pipeline)

0.5.4 - 2021-06-23

  • Speed up Ilastik image creation

0.5.3 - 2021-06-22

  • Fix CSV/FCS export

0.5.2 - 2021-06-15

  • Fix networkx node attribute export
  • Remove object_ prefix from default directory names
  • Speed up intensity measurement (use scipy.ndimage for aggregation)

0.5.1 - 2021-06-10

  • Version bumps of tifffile, xtiff
  • Preprocessing/postprocessing parameter support for DeepCell

0.5.0 - 2021-06-03

  • Module restructuring
  • PyPI package release
  • CLI refactoring, --version option
  • Improved documentation (API documentation is w.i.p.)
  • Export to OME-TIFF, CSV, FCS, AnnData, graph file formats
  • Match related files by name rather than alphabetical order
  • Customizable pixel/channel aggregation strategies
  • Many more small bug fixes & improvements

0.4.0 - 2021-05-27

  • Python API cleanup
  • Added DeepCell segmentation support

0.3.7 - 2021-05-20

  • Automatic SCM versioning
  • Steinbock version file checks
  • Renamed steinbock panel columns
  • Improved Docker container Python package setup
  • Combined kNN/distance-thresholded graph generation

0.3.6 - 2021-04-29

  • Make panel channel label values optional
  • Rename panel columns metal, name to id, label

0.3.5 - 2021-04-29

  • Minor bug fixes and performance improvements
  • Separated IMC panel/image preprocessing to allow for easier channel filtering

0.3.4 - 2021-04-27

  • #6 Panel creation from .mcd/.txt files
  • #9 Improved documentation on Ilastik feature selection
  • #10 Fixed Ilastik class label colors
  • #11 Simplified command-line interface

0.3.3 - 2021-04-21

New functionality, bug fixes, documentation improvements

Added:

  • ZIP archive support for IMC data (closes #2)
  • Ilastik channel ordering & grouping (closes #3)
  • Run container as non-privileged user (fixes #4)

0.3.2 - 2021-04-19

New functionality, bug fixes, documentation improvements

Added:

  • Mask matching
  • IMC panel pass-through
  • Generalized object segmentation
  • Hardened image loading to allow for tiles of size 1 in one dimension

0.3.1 - 2021-04-18

Documentation, minor improvements, fix memory leaks & stitching

0.3.0 - 2021-04-16

CLI refactoring, mosaic tooling

0.2.0 - 2021-04-12

CLI refactoring, removed imctoolkit dependency

Added:

  • Support for "raw" IMC panels
  • Additional user input validation
  • Mean channel in Ilastik images/crops
  • Additional progress bars/indicators
  • Measurements for cell regionprops
  • Measurements for cell distances/graphs

0.1.0 - 2021-04-08

Initial release for beta testing