BioimageAnalysisCoreWEHI/napari_lattice issues and pull requests

#100 - Migrate to bioio from aicsimageio

Issue - State: open - Opened by pr4deepr 25 days ago

#100 - Migrate to bioio from aicsimageio

Issue - State: open - Opened by pr4deepr 25 days ago

#99 - Remove napari-aicsimageio dependency

Issue - State: open - Opened by pr4deepr 25 days ago

#99 - Remove napari-aicsimageio dependency

Issue - State: open - Opened by pr4deepr 25 days ago

#98 - Fix_dependency

Pull Request - State: closed - Opened by pr4deepr 27 days ago - 6 comments

#98 - Fix_dependency

Pull Request - State: closed - Opened by pr4deepr 27 days ago - 6 comments

#97 - Plugin installation issues: pydantic and napari-aiscimageio

Issue - State: open - Opened by pr4deepr 29 days ago - 5 comments
Labels: bug

#96 - Better integrated dimension labels

Issue - State: open - Opened by multimeric 3 months ago
Labels: refactoring

#95 - Faster CI

Pull Request - State: closed - Opened by multimeric 3 months ago - 1 comment

#94 - Speed up CI

Issue - State: closed - Opened by multimeric 3 months ago - 1 comment

#93 - Install docs

Pull Request - State: closed - Opened by multimeric 4 months ago - 9 comments

#92 - Detect cropping outside of the image

Issue - State: closed - Opened by multimeric 4 months ago - 5 comments

#91 - Shape selector

Pull Request - State: closed - Opened by multimeric 4 months ago - 17 comments

#90 - Better ROI selection UI

Issue - State: closed - Opened by multimeric 5 months ago - 4 comments

#89 - Add openCL conda instructions

Pull Request - State: closed - Opened by multimeric 5 months ago - 1 comment

#88 - Add recipe for core package

Pull Request - State: open - Opened by multimeric 5 months ago

#87 - Build conda package

Issue - State: open - Opened by multimeric 5 months ago - 7 comments

#86 - tracking (Feature)

Issue - State: open - Opened by pr4deepr 5 months ago
Labels: enhancement

#85 - Fix 66 v2

Pull Request - State: closed - Opened by multimeric 5 months ago - 2 comments

#84 - Better conversion from napari Shapes to Rois

Pull Request - State: closed - Opened by multimeric 5 months ago - 7 comments

#83 - Auto publish to PyPI, Github release and docs on tag

Pull Request - State: closed - Opened by multimeric 5 months ago - 8 comments

#82 - Final frame fix

Pull Request - State: closed - Opened by DrLachie 6 months ago

#81 - Automatic doc building

Issue - State: closed - Opened by multimeric 6 months ago

#80 - Errors when final frame is incomplete

Issue - State: closed - Opened by DrLachie 6 months ago - 11 comments

#79 - ROIs defined on CZI MIPs are rotated

Issue - State: open - Opened by DrLachie 6 months ago

#78 - physical_pixel_size

Issue - State: closed - Opened by DrLachie 6 months ago

#77 - Unify param names

Pull Request - State: closed - Opened by DrLachie 6 months ago - 7 comments

#76 - cropping_napari_errors (duplicate of 63)

Issue - State: closed - Opened by pr4deepr 6 months ago - 5 comments

#75 - fix for roi indexing

Pull Request - State: closed - Opened by DrLachie 6 months ago

#74 - Debugging developer docs

Issue - State: open - Opened by multimeric 6 months ago - 1 comment

#73 - Make the Python API and CLI parameters have uniform names

Issue - State: closed - Opened by multimeric 6 months ago - 1 comment

#72 - combinging yaml and cli arguments causes error

Issue - State: closed - Opened by DrLachie 6 months ago

#71 - saving images leading to memory issues

Issue - State: open - Opened by pr4deepr 6 months ago - 3 comments
Labels: bug

#70 - Integrate cropping into the same code paths

Issue - State: open - Opened by multimeric 6 months ago

#69 - Enforce pydantic < 3

Pull Request - State: closed - Opened by multimeric 6 months ago

#68 - Fix #66

Pull Request - State: closed - Opened by multimeric 6 months ago - 8 comments

#67 - Docs v2

Pull Request - State: closed - Opened by multimeric 6 months ago

#66 - crop with workflow processing only first ROI

Issue - State: closed - Opened by pr4deepr 6 months ago - 2 comments
Labels: bug

#65 - Use pydantic compatibility layer

Pull Request - State: closed - Opened by multimeric 6 months ago

#64 - Fix release process

Issue - State: closed - Opened by multimeric 6 months ago

#63 - Small ROI Bug

Issue - State: closed - Opened by multimeric 6 months ago - 5 comments

#62 - Docs

Pull Request - State: closed - Opened by multimeric 6 months ago

#61 - Dependencies

Pull Request - State: open - Opened by multimeric 7 months ago

#60 - Better logging

Pull Request - State: open - Opened by multimeric 7 months ago

#59 - GitHub Pages Website

Issue - State: closed - Opened by multimeric 7 months ago - 2 comments

#58 - Add an imaris writer / ome.ngff writer

Issue - State: open - Opened by multimeric 7 months ago - 1 comment

#57 - Support Napari 0.5+

Issue - State: closed - Opened by multimeric 7 months ago

#56 - Bump conda-incubator/setup-miniconda from 2 to 3

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies, github_actions

#55 - Fix pip related requirements issue

Issue - State: closed - Opened by pr4deepr over 1 year ago - 12 comments
Labels: bug

#54 - Can this method applied to the Image captured by the Elyra lattice SIM (zeiss)?

Issue - State: closed - Opened by cindy12-gao over 1 year ago - 1 comment

#53 - Use clij2-fft for deconvolution using opencl

Issue - State: open - Opened by pr4deepr over 1 year ago
Labels: enhancement

#52 - Export yaml config from plugin for use on CLI

Issue - State: open - Opened by pr4deepr over 1 year ago
Labels: enhancement

#51 - napari hub listing

Issue - State: closed - Opened by pr4deepr over 1 year ago - 1 comment
Labels: documentation, github_actions

#50 - Migrate the GUI to `magicgui` dataclasses

Issue - State: open - Opened by multimeric over 1 year ago
Labels: enhancement

#49 - Migrate to Pydantic + Typer integration

Issue - State: open - Opened by multimeric over 1 year ago
Labels: enhancement

#48 - dealing with moving ROIs/cells or ROIs from tracking

Issue - State: open - Opened by pr4deepr over 1 year ago - 1 comment
Labels: enhancement

#47 - Pydantic Rework

Pull Request - State: closed - Opened by multimeric over 1 year ago - 153 comments

#46 - Bump actions/checkout from 2 to 4

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies, github_actions

#45 - Update README.md

Pull Request - State: open - Opened by DrLachie over 1 year ago

#44 - Package discovery error with new setuptools

Issue - State: closed - Opened by kaitsull over 1 year ago - 3 comments

#43 - processing image as tiles

Issue - State: open - Opened by pr4deepr over 1 year ago - 1 comment
Labels: enhancement

#42 - deconvolution add info in documentation

Issue - State: open - Opened by pr4deepr over 1 year ago
Labels: documentation

#41 - Using xarray instead of dask array

Issue - State: closed - Opened by pr4deepr over 1 year ago - 2 comments
Labels: enhancement

#40 - use skimage for reading psf tiff files

Pull Request - State: closed - Opened by pr4deepr over 1 year ago - 8 comments

#39 - Maximum aicsimageio

Pull Request - State: open - Opened by multimeric over 1 year ago

#38 - Re-pin tifffile, and make aicsimageio consistent

Pull Request - State: open - Opened by multimeric over 1 year ago

#37 - remove duplicate dependencies

Pull Request - State: closed - Opened by pr4deepr over 1 year ago - 2 comments

#36 - Use napari affine transform for live deskew

Issue - State: open - Opened by pr4deepr over 1 year ago
Labels: enhancement

#35 - Dependency checks

Pull Request - State: closed - Opened by multimeric over 1 year ago - 1 comment

#34 - Custom error types

Issue - State: open - Opened by multimeric over 1 year ago
Labels: refactoring

#33 - Apply automatic formatting

Issue - State: open - Opened by multimeric over 1 year ago
Labels: refactoring

#32 - Move the LatticeData defaults from the CLI

Issue - State: closed - Opened by multimeric over 1 year ago
Labels: refactoring

#31 - Refactor the deconvolution parameters into a separate class

Issue - State: closed - Opened by multimeric over 1 year ago
Labels: refactoring

#30 - Type annotations throughout

Issue - State: open - Opened by multimeric over 1 year ago
Labels: refactoring

#29 - Split Napari from Core

Pull Request - State: closed - Opened by multimeric over 1 year ago - 13 comments
Labels: enhancement, refactoring

#28 - 1. Separating out batch processing and napari options

Issue - State: closed - Opened by pr4deepr over 1 year ago
Labels: refactoring

#27 - code refactoring

Issue - State: open - Opened by pr4deepr almost 2 years ago
Labels: enhancement, refactoring

#26 - Bump actions/checkout from 2 to 3

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 2 comments
Labels: dependencies, github_actions

#25 - Bump chanzuckerberg/napari-hub-preview-action from 0.1.5 to 0.1.6

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies, github_actions

#24 - Orthogonal interpolation

Pull Request - State: closed - Opened by pr4deepr about 2 years ago - 6 comments

#23 - Bump codecov/codecov-action from 1 to 3

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies, github_actions

#22 - Bump actions/setup-python from 2 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies, github_actions

#21 - Bump actions/checkout from 2 to 3

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies, github_actions

#20 - For hpc

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

#19 - opencl deconvolution

Issue - State: open - Opened by pr4deepr over 2 years ago

#18 - Use 'logging' instead of 'print' statements

Issue - State: open - Opened by pr4deepr over 2 years ago - 3 comments
Labels: enhancement

#17 - Using "register_function" to add custom workflows

Issue - State: open - Opened by pr4deepr over 2 years ago - 3 comments
Labels: enhancement, help wanted

#16 - Deskewing artefact

Issue - State: closed - Opened by pr4deepr over 2 years ago - 20 comments
Labels: bug

#15 - fixing documentation

Issue - State: closed - Opened by pr4deepr over 2 years ago
Labels: documentation

#14 - add option for saving deskewed and deconvolved data

Issue - State: open - Opened by pr4deepr over 2 years ago
Labels: enhancement

#13 - ringing artefact from deconvolution

Issue - State: closed - Opened by pr4deepr over 2 years ago - 3 comments
Labels: bug

#12 - Use config file for no GUI processing

Issue - State: closed - Opened by pr4deepr over 2 years ago - 5 comments
Labels: enhancement

#11 - return multichannel image to use in cellpose worklfow

Issue - State: open - Opened by pr4deepr over 2 years ago
Labels: enhancement

#10 - implement cropping for skew in X direction

Issue - State: closed - Opened by pr4deepr over 2 years ago - 1 comment
Labels: bug, enhancement

#9 - implementing standard h5 saving?

Issue - State: open - Opened by pr4deepr over 2 years ago
Labels: enhancement

#8 - Does not recognise channels in czi file

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

#7 - H5 saving

Pull Request - State: closed - Opened by DrLachie over 2 years ago - 1 comment

#6 - Time end limitation

Issue - State: closed - Opened by brevid over 2 years ago - 1 comment

#5 - File naming

Issue - State: closed - Opened by brevid over 2 years ago - 1 comment

#4 - Make tests pass in github CI

Pull Request - State: closed - Opened by haesleinhuepf over 2 years ago - 1 comment

GitHub / BioimageAnalysisCoreWEHI/napari_lattice issues and pull requests