Ecosyste.ms: Issues

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GitHub / royerlab/dexp issues and pull requests

#136 - Fixed missing last frames fusion bug

Pull Request - State: closed - Opened by JoOkuma almost 2 years ago

#135 - fix dask client setup for deconvolution

Pull Request - State: closed - Opened by JoOkuma almost 2 years ago - 1 comment

#134 - add manual equalisation option for fusion

Pull Request - State: closed - Opened by JoOkuma almost 2 years ago

#133 - Add slicing support to zarr ome export

Pull Request - State: closed - Opened by JoOkuma almost 2 years ago

#132 - Fix dask-cuda import on windows

Pull Request - State: closed - Opened by JoOkuma about 2 years ago

#131 - CITATION.cff file

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

#130 - `deskew` command flip tuple length bug

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

#129 - FIX: rolling back dexp req

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

#128 - Merging `dev`

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

#127 - Bump mistune from 0.8.4 to 2.0.3 in /docs

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

#126 - Adding coverage and updating workflows

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

#125 - [fix] background removal crop/padding

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

#124 - Docs update

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

#123 - dev to master branch

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

#122 - [feature] refactoring fuse command

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

#121 - [feature] refactoring deconv cli

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

#120 - [bug] classic deskwing function

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

#119 - Updated README.md

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

#118 - [fix] refactoring `dispatch_data_to_backend` function path

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

#117 - Installation on Windows fails

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

#116 - [feature] added clear control time metadata

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

#115 - [fix] tensorstore open relative path

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

#114 - Minor improvements to `blind_deconvolution`

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

#113 - cleaning up dexp cli

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

#112 - Adding background command

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

#111 - Adding background command

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

#110 - Merging changes from master to dev

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

#109 - adding dexp generic function command

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

#108 - Improved dexp segm and view

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

#107 - Add dexp command to execute generic functions with dask and cupy

Pull Request - State: closed - Opened by JoOkuma almost 3 years ago - 1 comment

#106 - Remove `eval` and `exec` usages

Issue - State: open - Opened by JoOkuma almost 3 years ago
Labels: bug, enhancement, good first issue

#105 - Added multi-scale dexp -> ome zarr conversion

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

#104 - Added sum of intensities to segmentation

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

#103 - New click parsing auxiliary functions

Pull Request - State: closed - Opened by JoOkuma almost 3 years ago - 2 comments

#102 - Updated parse devices function name

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

#101 - Update click cli logic

Issue - State: closed - Opened by JoOkuma almost 3 years ago

#100 - Added segmentation function

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

#99 - Added rsqrt and cupy fuse to butterworth denoising

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

#98 - Improve noise2self j-invariant optimization

Issue - State: open - Opened by JoOkuma almost 3 years ago
Labels: enhancement

#97 - Added butterworth denoiser from Aydin

Pull Request - State: closed - Opened by JoOkuma almost 3 years ago - 1 comment

#96 - Changes to dask compute setup

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

#95 - Denoise code almost ready to integrate!

Pull Request - State: closed - Opened by royerloic almost 3 years ago - 2 comments

#94 - Changed beads detection threshold method

Pull Request - State: closed - Opened by JoOkuma almost 3 years ago - 1 comment

#93 - Updated API docs generation

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

#92 - Fixing docs req and removing warnings

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

#91 - Added fromraw command to fix frame alignment.

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

#90 - Added beads removal to fusion

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

#89 - Added `fromraw` command

Pull Request - State: closed - Opened by JoOkuma almost 3 years ago - 1 comment

#88 - Added histogram computation

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

#87 - Adding `dexp` prefix to commands

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

#86 - Added simplified TIF dataset API

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

#85 - Added option to read or write stabilization model

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

#84 - Updated dependencies

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

#83 - added pyopencl to installation instructions

Pull Request - State: closed - Opened by haesleinhuepf almost 3 years ago - 1 comment

#82 - Adding custom processing docs

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

#81 - Implemented axis wise morph operations

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

#80 - Added tutorial of command line processing.

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

#79 - Minor changes to deconv demo

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

#78 - What is the complete command format when running the program?

Issue - State: closed - Opened by ornekofbf about 3 years ago - 3 comments

#77 - Adding WTH to fuse operation

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

#76 - Adding code coverage

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

#75 - Minor fixes

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

#74 - Added basic math morphology functions

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

#73 - Updated docs requirements

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

#72 - Added how-to guide

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

#71 - Normalization refactor

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

#70 - Check redundant `warp` tests

Issue - State: open - Opened by JoOkuma about 3 years ago
Labels: enhancement, good first issue

#69 - Changing files organization and refactoring tests

Pull Request - State: closed - Opened by JoOkuma about 3 years ago - 2 comments

#68 - Improving function imports

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

#67 - Check CI Linting results

Issue - State: open - Opened by JoOkuma about 3 years ago

#66 - Added pre-commit to repo

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

#65 - Fixing docs build

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

#64 - Added ADMM regularized deconvolution

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

#63 - Added option to fuse two views from different cameras.

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

#62 - Fixing docs deploy

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

#61 - Updating docs, missing descriptions.

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

#60 - Deskew for single views without fusion

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

#59 - Need to read multipage TIFF files saved by MicroManager and save to Zarr

Issue - State: open - Opened by BinYangOptics over 3 years ago - 1 comment

#58 - Added commands to extract PSF

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

#57 - testing tensorstore fusion

Pull Request - State: closed - Opened by JoOkuma over 3 years ago - 1 comment

#56 - Added padding parameter to fusion

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

#55 - Fixing num workers parameter setup

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

#54 - Fixing docs build and closing #9

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

#53 - Removing circular import of CLI defaults

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

#52 - Cleaning up some dependencies

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

#51 - OME-zarr support

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

#50 - Added automatic cropping command

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

#49 - Updated stabilization

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

#48 - Added Zarr to Big Data Viewer format

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

#47 - Reverted copying operations to allow multiple workers

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

#46 - Removed dask distributed usage from fusion when using a single device

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

#44 - Added option to fuse views from a single camera (only two images)

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

#42 - docs readme updated

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

#37 - Issue to discuss our metadata format

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

#36 - Add parent argument for dexp dataset class

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

#31 - Suggestion for dexp classes importing.

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

#17 - Circular import within dexp.cli module

Issue - State: closed - Opened by AhmetCanSolak almost 4 years ago
Labels: bug

#12 - dexp.processing.backends module needs docstring improvements

Issue - State: closed - Opened by AhmetCanSolak almost 4 years ago - 1 comment
Labels: documentation

#9 - VolumeRenderer cannot import gputools

Issue - State: closed - Opened by AhmetCanSolak almost 4 years ago - 3 comments
Labels: bug

#3 - dexp tiff viewer

Issue - State: closed - Opened by pranathivemuri over 5 years ago - 3 comments