Ecosyste.ms: Issues

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GitHub / tlambert03/microsim issues and pull requests

#80 - more ground truth sources

Issue - State: open - Opened by tlambert03 about 1 month ago

#79 - feat: scaling each light source by the respective power

Pull Request - State: closed - Opened by federico-carrara 2 months ago - 4 comments
Labels: enhancement

#78 - feat: adding Identity PSF modality

Pull Request - State: closed - Opened by federico-carrara 2 months ago - 1 comment
Labels: enhancement

#77 - fix: fix key again

Pull Request - State: closed - Opened by tlambert03 3 months ago - 2 comments

#76 - ci(pre-commit.ci): autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 3 months ago - 1 comment

#75 - fix: typos

Pull Request - State: closed - Opened by tlambert03 3 months ago - 1 comment

#74 - refactor: rewrite simulation stages, improve optical config spectral considerations

Pull Request - State: closed - Opened by tlambert03 3 months ago - 3 comments

#73 - Tests failing in CI

Issue - State: open - Opened by github-actions[bot] 4 months ago
Labels: reusable-test-failure

#72 - ci(pre-commit.ci): autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 4 months ago - 1 comment

#71 - refactor: remove pint from models

Pull Request - State: closed - Opened by tlambert03 4 months ago - 2 comments

#70 - Unit of measure of Spectrum intensity

Issue - State: closed - Opened by federico-carrara 4 months ago - 1 comment

#69 - Fix cosem images download error

Pull Request - State: closed - Opened by veegalinova 4 months ago - 2 comments

#68 - todo: maybe just use dask throughout

Issue - State: open - Opened by tlambert03 5 months ago

#67 - fix: allowing None type for 'CosemDataset' attributes

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

#66 - Validation of CosemDataset attributes raises errors

Issue - State: open - Opened by federico-carrara 5 months ago - 2 comments

#65 - fix: fix cosem fetch

Pull Request - State: closed - Opened by tlambert03 5 months ago

#64 - URL issue with scraping of COSEM data

Issue - State: closed - Opened by federico-carrara 5 months ago - 2 comments

#63 - Implementing Illumination/Irradiance as a (W, C, Z, Y, X) array

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

#62 - Tests failing in CI

Issue - State: closed - Opened by github-actions[bot] 5 months ago
Labels: reusable-test-failure

#61 - Tests failing in CI

Issue - State: closed - Opened by github-actions[bot] 5 months ago
Labels: reusable-test-failure

#60 - ci(pre-commit.ci): autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago - 1 comment

#59 - Documentation for excitation and emission code + a bug fix.

Pull Request - State: closed - Opened by ashesh-0 5 months ago - 6 comments

#58 - add init_forbid_extra in pydantic.mypy settings

Pull Request - State: closed - Opened by tlambert03 5 months ago - 1 comment

#57 - fix: fixed typo (from 'placemen' to 'placement')

Pull Request - State: closed - Opened by federico-carrara 5 months ago

#56 - fix: fix for redhat

Pull Request - State: closed - Opened by tlambert03 5 months ago - 1 comment
Labels: bug

#53 - fix: remove caching on bins

Pull Request - State: closed - Opened by tlambert03 5 months ago - 1 comment

#52 - todo: expose exposure time

Issue - State: open - Opened by tlambert03 5 months ago

#51 - build: pin numpy to <2 until next tensorstore release

Pull Request - State: closed - Opened by tlambert03 5 months ago - 5 comments

#50 - feat: add cosem models, downloading, caching, binning, and tests

Pull Request - State: closed - Opened by tlambert03 6 months ago - 1 comment

#49 - feat: add ndview convenience

Pull Request - State: closed - Opened by tlambert03 6 months ago

#48 - feat: pull neuron ground truths from allen brain

Pull Request - State: closed - Opened by tlambert03 6 months ago - 1 comment
Labels: enhancement

#47 - TODO: add cli

Issue - State: open - Opened by tlambert03 6 months ago

#46 - docs: Overview of various stages.

Pull Request - State: closed - Opened by tlambert03 6 months ago - 1 comment

#45 - ci: try self-hosted for cupy

Pull Request - State: closed - Opened by tlambert03 6 months ago - 1 comment

#44 - Establish dimension conventions, pass dimensions through more explicitly

Pull Request - State: closed - Opened by tlambert03 6 months ago - 2 comments

#42 - ci(pre-commit.ci): autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago - 1 comment

#41 - feat: add caching

Pull Request - State: closed - Opened by tlambert03 6 months ago - 2 comments

#40 - feat: allow loading optical configs from fpbase, general refactor of optical configs

Pull Request - State: closed - Opened by tlambert03 6 months ago - 4 comments

#39 - comments added to emission_events.py

Pull Request - State: closed - Opened by ashesh-0 6 months ago - 2 comments

#38 - fix cupy

Pull Request - State: closed - Opened by tlambert03 6 months ago - 3 comments

#37 - feat: add pint quantities to more fields

Pull Request - State: closed - Opened by tlambert03 6 months ago - 1 comment

#35 - feat: support multi-channel, multi-fluorophore simulations

Pull Request - State: closed - Opened by ashesh-0 6 months ago - 12 comments
Labels: enhancement

#33 - Overall schema for multi-fluorophore integration.

Pull Request - State: closed - Opened by ashesh-0 6 months ago - 2 comments

#32 - feat: add direct from ground truth

Pull Request - State: closed - Opened by tlambert03 6 months ago - 2 comments

#30 - feat: swappable fft backends, including torch and jax

Pull Request - State: closed - Opened by tlambert03 7 months ago - 2 comments

#28 - feat: higher level psf caching

Pull Request - State: closed - Opened by tlambert03 7 months ago - 1 comment

#27 - Update ci, prep for release to pypi

Pull Request - State: closed - Opened by tlambert03 7 months ago - 1 comment

#26 - feat: cache psf

Pull Request - State: closed - Opened by tlambert03 7 months ago

#25 - Memoization scheme

Issue - State: open - Opened by tlambert03 7 months ago

#24 - ci(pre-commit.ci): autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago

#23 - Feature: allow PSFs to be saved and reused

Issue - State: closed - Opened by tlambert03 7 months ago - 6 comments

#22 - Integrate fluorophore into the simulation.

Issue - State: closed - Opened by ashesh-0 7 months ago - 2 comments

#21 - TODO: meta-issue

Issue - State: open - Opened by tlambert03 7 months ago

#20 - problem with render() design

Issue - State: open - Opened by tlambert03 7 months ago

#19 - feat: use SimBaseModel and add float precision setting

Pull Request - State: closed - Opened by tlambert03 7 months ago

#18 - feat: cosem Sample

Pull Request - State: closed - Opened by tlambert03 7 months ago - 2 comments

#17 - cosem and cleanup

Pull Request - State: closed - Opened by tlambert03 8 months ago

#16 - Smaller psf

Pull Request - State: closed - Opened by tlambert03 8 months ago

#15 - ci(dependabot): bump codecov/codecov-action from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#14 - ci(dependabot): bump actions/setup-python from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#13 - ci(dependabot): bump softprops/action-gh-release from 1 to 2

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#12 - Reorganize code

Pull Request - State: closed - Opened by tlambert03 8 months ago - 1 comment

#11 - Fix import and formatting issues in multiple files

Pull Request - State: closed - Opened by tlambert03 8 months ago - 1 comment

#10 - ci(dependabot): bump styfle/cancel-workflow-action from 0.11.0 to 0.12.0

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#9 - ci(dependabot): bump actions/checkout from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#8 - ci(pre-commit.ci): autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#7 - update precommit

Pull Request - State: closed - Opened by tlambert03 over 1 year ago

#6 - use mypyc for bresenham

Pull Request - State: closed - Opened by tlambert03 over 1 year ago

#5 - ci(pre-commit.ci): autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#4 - [test-bot] pip install --pre is failing

Issue - State: closed - Opened by github-actions[bot] over 1 year ago
Labels: bug

#3 - [test-bot] pip install --pre is failing

Issue - State: closed - Opened by github-actions[bot] over 1 year ago
Labels: bug

#2 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#1 - Updated README

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