Ecosyste.ms: Issues

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GitHub / mehta-lab/waveorder issues and pull requests

#174 - Run CI on multiple platforms

Issue - State: open - Opened by ziw-liu 3 months ago

#173 - Pin numpy <2

Pull Request - State: closed - Opened by ziw-liu 3 months ago

#172 - Severe artifacts and blur in 2D phase reconstruction

Issue - State: open - Opened by ziw-liu 3 months ago - 1 comment
Labels: bug

#171 - Merge `alg-dev` into main ahead of release

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

#170 - Vector-optics birefringence reconstruction prototype

Pull Request - State: open - Opened by talonchandler 3 months ago

#169 - New release

Issue - State: open - Opened by ziw-liu 4 months ago - 3 comments
Labels: meta

#168 - Bump Python

Pull Request - State: closed - Opened by ziw-liu 4 months ago

#167 - Bump Python

Issue - State: closed - Opened by ziw-liu 4 months ago

#166 - Fluorescence deconvolution issues

Issue - State: open - Opened by Alpaca233 4 months ago - 1 comment
Labels: documentation, question

#165 - Authorship and release updates

Pull Request - State: closed - Opened by talonchandler 4 months ago

#164 - Phase reconstruction is invariant to voxel-size

Pull Request - State: closed - Opened by talonchandler 6 months ago
Labels: bug

#163 - Non-negative fluorescence output?

Issue - State: open - Opened by ziw-liu 6 months ago - 2 comments

#162 - fix bug finding focus in stack with only one slice

Pull Request - State: closed - Opened by ieivanov 7 months ago - 2 comments
Labels: bug

#161 - 3D phase reconstruction should not use reflection padding

Issue - State: open - Opened by talonchandler 7 months ago - 2 comments
Labels: bug

#160 - PTI example jupyter notebook to script and .html

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

#159 - Update a single PTI example notebook

Pull Request - State: closed - Opened by talonchandler 7 months ago - 3 comments
Labels: documentation

#158 - Link BIA data next to examples

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

#157 - Prepare README for 2.0.0

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

#156 - M1 installation documentation

Pull Request - State: closed - Opened by talonchandler 7 months ago
Labels: documentation

#155 - Document order-dependent scripts

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

#154 - Tests fail on macbook with incomplete MPS support

Issue - State: open - Opened by talonchandler 7 months ago - 6 comments
Labels: GPU

#153 - Update background estimation to use torch

Pull Request - State: closed - Opened by ziw-liu 9 months ago - 1 comment
Labels: enhancement, GPU

#152 - [Bug] Overlapping rings in phase transfer function

Issue - State: open - Opened by ziw-liu about 1 year ago - 5 comments
Labels: bug

#151 - Phase transfer function is numerically small

Issue - State: open - Opened by ziw-liu about 1 year ago - 3 comments
Labels: bug

#150 - Device agnostic compute for polarization

Pull Request - State: closed - Opened by ziw-liu about 1 year ago - 3 comments
Labels: enhancement, GPU

#149 - `waveorder` handles all rotational quantities (including retardance) in radians

Pull Request - State: closed - Opened by talonchandler about 1 year ago - 2 comments

#148 - Add rotate and flip orientation options to `waveorder` options

Pull Request - State: closed - Opened by talonchandler about 1 year ago - 3 comments

#147 - Simplify dependencies

Pull Request - State: closed - Opened by talonchandler about 1 year ago

#146 - Unused `pycromanager>=0.13.2` requirement

Issue - State: closed - Opened by ieivanov about 1 year ago

#145 - 5D padding

Pull Request - State: closed - Opened by edyoshikun about 1 year ago - 2 comments

#144 - Support GPUs via `torch`

Issue - State: open - Opened by talonchandler about 1 year ago - 1 comment
Labels: enhancement, GPU

#143 - Remove `waveorder_reconstructor` and `waveorder_simulator` files

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

#142 - Move PTI reconstructions to `torch` and `models`

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

#141 - Fix readme figure

Pull Request - State: closed - Opened by talonchandler about 1 year ago

#140 - Divide by zero during phase normalization

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

#139 - Torch warning about copying tensors

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

#138 - Specify meshgrid indexing order

Pull Request - State: closed - Opened by talonchandler about 1 year ago

#137 - torch meshgrid warning

Issue - State: closed - Opened by talonchandler about 1 year ago

#136 - close figure after saving

Pull Request - State: closed - Opened by ieivanov about 1 year ago

#135 - Fix threshold-free focus-finding edge case

Pull Request - State: closed - Opened by talonchandler about 1 year ago

#134 - Remove `__init__` imports

Pull Request - State: closed - Opened by talonchandler about 1 year ago - 1 comment

#133 - waveorder changes matplotlib backend at import

Issue - State: closed - Opened by ieivanov about 1 year ago - 2 comments

#131 - Match parameters to simplify `recOrder`-`waveorder` interface

Pull Request - State: closed - Opened by talonchandler about 1 year ago

#130 - Make `torch` optional dependency?

Issue - State: closed - Opened by ieivanov about 1 year ago - 4 comments

#129 - Focus-finding features

Issue - State: closed - Opened by talonchandler about 1 year ago

#128 - `isotropic_fluorescent_thick_3d` model

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

#127 - Rename model from `anisotropic_thin` to `oriented_thick`

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

#126 - Adding padding and tile processing

Pull Request - State: closed - Opened by edyoshikun over 1 year ago - 4 comments

#125 - Remove duplicate test

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

#124 - Add option for axial flip of `phase_thick_3d` transfer function

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

#123 - `illumination_wavelength` -> `wavelength_illumination`

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

#122 - Migrate fluorescence reconstructions to `torch` and `model`-based structure

Issue - State: open - Opened by talonchandler over 1 year ago - 4 comments
Labels: enhancement

#121 - `alg-dev` branch merge to `main`

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

#119 - Remove kwargs from reconstructions

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

#118 - Prepare polarization algorithms for integration with `recOrder`

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

#117 - Phase 2D + 3D refactor

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

#116 - Pin README links

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

#115 - Fix link to example

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

#114 - Prepare for `waveorder==1.0.0` release

Pull Request - State: closed - Opened by talonchandler over 1 year ago - 5 comments

#112 - Removing I/O module

Issue - State: closed - Opened by ziw-liu over 1 year ago - 5 comments

#111 - PR docs

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

#110 - New Stokes and Mueller module

Pull Request - State: closed - Opened by talonchandler over 1 year ago - 16 comments

#109 - Add .git-blame-ignore-revs

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

#108 - Replace OpenCV with pillow

Pull Request - State: closed - Opened by ziw-liu over 1 year ago - 2 comments
Labels: enhancement

#107 - `opencv-python` is taking >30 minutes to build on M1

Issue - State: closed - Opened by talonchandler over 1 year ago - 5 comments

#106 - README figure is low-res and transparent

Issue - State: closed - Opened by talonchandler over 1 year ago - 2 comments
Labels: documentation

#105 - README copy edits

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

#104 - uPTI -> PTI; black formatting; improved comments

Pull Request - State: closed - Opened by talonchandler over 1 year ago - 3 comments

#102 - Slow birefringence reconstruction for z-stacks

Issue - State: closed - Opened by edyoshikun over 1 year ago - 6 comments

#101 - Improve README.md

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

#100 - Improve README.md

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

#99 - Drop 3.7 and add 3.8, 3.9, 3.10

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

#98 - Bump Python version

Issue - State: closed - Opened by ziw-liu almost 2 years ago
Labels: enhancement

#97 - `napari.Viewer()` fails after `import waveorder` in OnDemand session

Issue - State: closed - Opened by talonchandler almost 2 years ago - 1 comment

#96 - Added example for multiple input deconvolution

Pull Request - State: closed - Opened by Soorya19Pradeep almost 2 years ago - 3 comments

#95 - `WaveorderReader` uses `glob` to read a folder of ome-tiffs

Issue - State: closed - Opened by talonchandler almost 2 years ago - 6 comments

#94 - `WaveorderWriter` is not compatible with `napari-ome-zarr` reader

Issue - State: closed - Opened by talonchandler almost 2 years ago - 6 comments
Labels: bug

#93 - `WaveorderReader` should give more informative error messages

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

#92 - Find focus by optimizing a transverse spatial frequency band

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

#91 - `lambda_illu`, `NA_obj`, and `NA_illu` names can be improved

Issue - State: closed - Opened by talonchandler almost 2 years ago - 1 comment

#90 - Odd-sized dimensions use incorrect frequency coordinates

Issue - State: closed - Opened by talonchandler almost 2 years ago - 1 comment

#89 - estimate focus slice during 2D phase from brightfield reconstruction

Issue - State: closed - Opened by mattersoflight almost 2 years ago - 1 comment

#88 - Replace custom CuPy implementation of SciPy APIs

Issue - State: open - Opened by ziw-liu almost 2 years ago - 3 comments
Labels: enhancement

#87 - Rename `master` to `main`

Issue - State: closed - Opened by ziw-liu almost 2 years ago
Labels: meta

#86 - Pin pywavelets version

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

#85 - improve readability of waveOrder

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

#84 - BSD 3-clause

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

#83 - Don't delete test data

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

#82 - Bump version to 1.0.0rc0

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

#81 - Fix typo and update contact info in `setup.py`

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

#80 - Update documentation of waveorder_reconstructor.py

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

#79 - Pycromanager data reader for WaveorderReader class

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

#78 - `setup.py` includes line: `python_requies = '==3.7'`

Issue - State: closed - Opened by talonchandler about 2 years ago

#76 - Waveorder multiprocessing scripts in example folder

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

#75 - multiprocess for QLIPP & deconvolution

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

#74 - updated documentation of waveorder_microscopy

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

#73 - multiprocess script refactoring, set default to run full job

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