Ecosyste.ms: Issues

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GitHub / NHPatterson/wsireg issues and pull requests

#74 - use opencv-python-headless rather than opencv-python

Pull Request - State: closed - Opened by NHPatterson 7 months ago

#73 - Fix error when passing a boolean mask

Pull Request - State: open - Opened by grst 8 months ago - 1 comment

#72 - how to apply manually matched point pairs?

Issue - State: open - Opened by inyeopjang 10 months ago

#70 - Output resolution is not respected

Issue - State: open - Opened by leorrose 11 months ago - 2 comments

#69 - Remove support for AICSIMAGEIO

Pull Request - State: closed - Opened by NHPatterson 12 months ago

#68 - Concatenating transformations across separate modalities

Issue - State: open - Opened by leorrose about 1 year ago

#67 - Asymmetrical images

Issue - State: open - Opened by leorrose about 1 year ago - 1 comment

#66 - Output file generated by transform_images is corrupted.

Issue - State: closed - Opened by grst over 1 year ago - 2 comments

#65 - Initial transformation

Issue - State: open - Opened by JingyeWang1998 over 1 year ago - 1 comment

#64 - Citation

Issue - State: open - Opened by KidElectric over 1 year ago - 1 comment

#63 - register_images() hangs when calling UpdateLargestPossibleRegion()

Issue - State: closed - Opened by conradfoo almost 2 years ago - 3 comments

#62 - Copy wsireg alignment scheme to rest of the channels from same modality?

Issue - State: closed - Opened by BokaiZhu over 2 years ago - 2 comments

#61 - unpin ITK with fix of `itk-elastix`, other small bug fixes

Pull Request - State: closed - Opened by NHPatterson over 2 years ago

#60 - Fix configuration save to include merge modalities

Pull Request - State: closed - Opened by NHPatterson over 2 years ago

#59 - PyCapsule_Import "_ITKCommonPython._C_API" is not valid

Issue - State: closed - Opened by BioinfoTongLI over 2 years ago - 4 comments

#58 - error calling wsi-reg on napari on windows

Issue - State: closed - Opened by alcrevenna over 2 years ago - 2 comments

#57 - Add convenience functionality to visualize registered images in `vizarr`/ `napari`

Issue - State: open - Opened by NHPatterson over 2 years ago
Labels: enhancement

#56 - error on napari plugin

Issue - State: closed - Opened by alcrevenna over 2 years ago - 5 comments

#55 - Fix CI errors around dask with test fixtures images.

Pull Request - State: closed - Opened by NHPatterson over 2 years ago

#54 - make config writing error-free, and make console script work

Pull Request - State: closed - Opened by NHPatterson over 2 years ago

#53 - Black formatting on last PR

Pull Request - State: closed - Opened by NHPatterson almost 3 years ago

#52 - Add plotting

Pull Request - State: closed - Opened by NHPatterson almost 3 years ago

#51 - keep shape spacing information after transformation

Pull Request - State: closed - Opened by NHPatterson almost 3 years ago

#50 - Failed Alignment of sequential stained samples

Issue - State: closed - Opened by rjesud almost 3 years ago - 9 comments

#49 - Register more than 2 images simultaneously?

Issue - State: closed - Opened by ajr82 almost 3 years ago - 2 comments

#48 - Update docs with more info

Pull Request - State: closed - Opened by NHPatterson almost 3 years ago

#46 - Upgrade RegShapes to QP geojson format

Pull Request - State: closed - Opened by NHPatterson almost 3 years ago

#45 - Refactoring major classes and reorganize docs and add more docstrings

Pull Request - State: closed - Opened by NHPatterson almost 3 years ago

#44 - Error after installing

Issue - State: closed - Opened by alcrevenna almost 3 years ago - 4 comments

#43 - Refactor and rewrite tiled image transform using `Tiler`

Pull Request - State: closed - Opened by NHPatterson almost 3 years ago

#42 - Major refactor of the RegImage class for extensibility

Pull Request - State: closed - Opened by NHPatterson almost 3 years ago

#41 - Remove modality

Pull Request - State: closed - Opened by NHPatterson almost 3 years ago

#40 - update tifffile and zarr versions

Pull Request - State: closed - Opened by NHPatterson almost 3 years ago

#39 - Update CI for automated pypi deployment

Pull Request - State: closed - Opened by NHPatterson almost 3 years ago

#38 - refactor to project for easier changes

Pull Request - State: closed - Opened by NHPatterson almost 3 years ago

#37 - Add draw_mask method to RegShapes

Pull Request - State: closed - Opened by NHPatterson almost 3 years ago

#36 - Add ability to mix data types in final merger

Pull Request - State: closed - Opened by NHPatterson about 3 years ago - 1 comment

#35 - add RegTransformSeq to chain transformations

Pull Request - State: closed - Opened by NHPatterson about 3 years ago

#33 - Cast all point data to double for operations in SimpleITK

Pull Request - State: closed - Opened by NHPatterson about 3 years ago

#32 - write with geojson extension

Pull Request - State: closed - Opened by NHPatterson about 3 years ago

#31 - Shapes and QuPath

Issue - State: closed - Opened by Michael-L-Miller about 3 years ago - 10 comments

#30 - Use `ome-types` to build OME data

Issue - State: open - Opened by NHPatterson over 3 years ago - 6 comments

#29 - Add logo

Pull Request - State: closed - Opened by NHPatterson over 3 years ago

#28 - Mixing dtypes / RGB in merged image files

Issue - State: closed - Opened by NHPatterson over 3 years ago
Labels: enhancement

#27 - fix transformation writing for attachment modalities closes #26

Pull Request - State: closed - Opened by NHPatterson over 3 years ago

#25 - Fix reading individual channels or select channels in zeiss czi files

Pull Request - State: closed - Opened by NHPatterson over 3 years ago

#24 - Fix config write

Pull Request - State: closed - Opened by NHPatterson over 3 years ago

#23 - Fix arraylike in config writer

Issue - State: closed - Opened by NHPatterson over 3 years ago

#22 - Numpy or Dask image array support

Issue - State: closed - Opened by rjesud over 3 years ago - 17 comments

#21 - Add writing merged and unmerged image versions optionally

Pull Request - State: closed - Opened by NHPatterson over 3 years ago
Labels: enhancement

#19 - Fixes error in transforming images merged by `add_merge_modalities`

Pull Request - State: closed - Opened by NHPatterson over 3 years ago

#18 - Update `RegImage` file type subclasses

Pull Request - State: closed - Opened by NHPatterson over 3 years ago

#17 - No exported ometiff and frozen progress

Issue - State: closed - Opened by rjesud over 3 years ago - 15 comments
Labels: bug, good first issue

#16 - Gigapixel WSI deformable registration

Issue - State: closed - Opened by omayrkhan over 3 years ago - 3 comments
Labels: question

#15 - use `aicsimageio` for Zeiss .czi images

Pull Request - State: closed - Opened by NHPatterson over 3 years ago

#10 - Use NetworkX to represent registration graph

Issue - State: open - Opened by NHPatterson over 3 years ago

#8 - Tifffile throws delayed import error

Issue - State: closed - Opened by JLrumberger over 3 years ago - 2 comments

#7 - Handling of `prepro_dict`

Issue - State: closed - Opened by manzt almost 4 years ago - 2 comments

#6 - Unifying `add_modality` API for code reuse

Issue - State: open - Opened by manzt almost 4 years ago - 1 comment

#5 - [WIP] Allow numpy array interfaces for `NumpyRegImage`

Pull Request - State: closed - Opened by manzt almost 4 years ago - 3 comments

#4 - Add handling of non-interleaved RGB images for most reg image subclasses

Pull Request - State: closed - Opened by NHPatterson almost 4 years ago - 2 comments

#3 - Add default `tile_size` for zarr writer

Pull Request - State: closed - Opened by manzt almost 4 years ago - 1 comment

#2 - improvements and many new features

Pull Request - State: closed - Opened by NHPatterson almost 4 years ago

#1 - update to v0.2.0

Pull Request - State: closed - Opened by NHPatterson almost 4 years ago