lumicks/pylake issues and pull requests

#704 - channel: support recalibrating force data

Pull Request - State: open - Opened by JoepVanlier 17 days ago

#703 - merge `release/1.5` back into `main`

Pull Request - State: closed - Opened by JoepVanlier 18 days ago

#702 - release: release pylake `v1.5.3`

Pull Request - State: closed - Opened by JoepVanlier 18 days ago

#701 - release: backport fixes and release pylake `1.4.2`

Pull Request - State: closed - Opened by JoepVanlier 18 days ago

#700 - deps: allow `numpy>=2`, add `python==3.13` to ci

Pull Request - State: closed - Opened by JoepVanlier 29 days ago

#699 - docs: rework force calibration documentation

Pull Request - State: open - Opened by JoepVanlier about 1 month ago

#698 - ci: make sure we used fixed seed in fixtures

Pull Request - State: closed - Opened by JoepVanlier about 1 month ago - 1 comment

#697 - docs: support surface calibration

Pull Request - State: open - Opened by JoepVanlier about 1 month ago - 1 comment

#696 - download: allow non-url characters in filenames

Pull Request - State: closed - Opened by JoepVanlier about 2 months ago

#695 - PowerSpectrum: improve diagnostic value power spectrum api

Pull Request - State: open - Opened by JoepVanlier about 2 months ago

#694 - calibration: expose diode calibration

Pull Request - State: closed - Opened by JoepVanlier about 2 months ago

#693 - slice: add `array` to `Slice`

Pull Request - State: closed - Opened by JoepVanlier 2 months ago

#692 - Don't forget to drop this line. Docs won't build with a dead link.

Issue - State: closed - Opened by aafkevandenberg 2 months ago

#691 - examples: kymo micron to bp conversion

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

#690 - dwelltime: add standard errors based on hessian approximation

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

#689 - ci: don't modify test parametrization during test

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

#688 - caching: centralize caching

Pull Request - State: open - Opened by JoepVanlier 3 months ago - 2 comments

#687 - confocal: fix bug with empty power channels

Pull Request - State: closed - Opened by JoepVanlier 3 months ago

#686 - api: add low level api for confocal objects / slice

Pull Request - State: closed - Opened by JoepVanlier 4 months ago - 1 comment

#685 - kymotrack: add `sample_from_channel`

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

#684 - adjustment: prevent division by zero

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

#683 - fdfit: add docstring to `Parameter`

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

#682 - slice: add option to highlight time region

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

#681 - fdfitter: fix inversion for the scalar case

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

#680 - tools: small fix to `run_notebooks`

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

#679 - merge `release/1.5` back into `main`

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

#678 - release: release Pylake v1.4.1

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

#677 - scan: allow loading truncated scans

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

#676 - release: Release Pylake v1.5.2

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

#675 - ci: some ci maintenance work

Pull Request - State: closed - Opened by JoepVanlier 4 months ago - 3 comments

#674 - Examples droplet fusion

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

#673 - Emulate numeric types for parameter classes

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

#672 - calibration: move force calibration items into more appropriate locations

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

#671 - docs: make all notebooks executable

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

#670 - testing: add small script to test notebooks we ship

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

#669 - tracker: allow widget backend

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

#668 - kymotrack: load photon counts from file

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

#667 - Bugfix: handle tuple of excluded ranges passed in

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

#666 - calibration: expose all relevant calibration parameters as properties

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

#665 - calibration: private api for exclusion/fit ranges

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

#664 - calibration: force calibration API pretty printing

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

#663 - examples: add hairpin unfolding fitting

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

#662 - force: provide better API for recalibrating offline

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

#661 - kymo: allow custom titles in `plot_with_channels`

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

#660 - zenodo: add `allow_overwrite` as parameter

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

#659 - file: populate calibration field when accessing force via square brackets

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

#658 - Update population_dynamics.rst

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

#657 - Update piezotracking.rst

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

#656 - Wrong return parametrs in the documentation for buoyancy_freq(

Issue - State: closed - Opened by bhlevca 6 months ago - 2 comments

#655 - merge release/1.5 to main

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

#654 - release: release Pylake v1.5.1

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

#653 - file: fix detector mapping bug

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

#652 - Update piezotracking.rst

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

#651 - tests: fix test for tracking `ImageStack`-based `Kymo`

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

#650 - docs: move gifs to lfs

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

#649 - Release pylake v1.5.0

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

#648 - docs: what's new for 1.5.0

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

#647 - video export: fix two bugs in video export

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

#646 - Support python 3.12 / notebook>=7 and drop support for python 3.9.

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

#645 - docs: small style fixes

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

#644 - tests: hash parameterized tests for shorter paths

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

#643 - merge bugfix back into `main`

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

#642 - fdfit: better error handling `parameter_trace()`

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

#641 - calibration: provide error estimates for kappa and Rd

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

#640 - ci: add option to serialize test dictionaries

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

#639 - docs: minor fixups

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

#638 - kymo: add `plot_with_channels`

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

#637 - plotting: rename to `downsample_to_frames`

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

#636 - calibration: expose an estimate of the local drag

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

#635 - calibration: make it easier to simulate model

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

#634 - plot_correlated: add option to not downsample the channel data

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

#633 - calibration: fix incorrect statistical backing calculation

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

#632 - Update installation instructions China

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

#631 - merge `1.4` back into `main`

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

#630 - imagestack: support two-color tiff stacks

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

#629 - docs: fix some small oversights in the documentation

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

#628 - Replace hardcoded names in `File.str`

Pull Request - State: closed - Opened by rpauszek 9 months ago

#627 - tests: force close tiff files

Pull Request - State: closed - Opened by JoepVanlier 9 months ago

#626 - release: release pylake v1.4.0

Pull Request - State: closed - Opened by JoepVanlier 9 months ago

#625 - some final tasks before release

Pull Request - State: closed - Opened by JoepVanlier 9 months ago

#624 - kymo: finding bead edges part 2

Pull Request - State: closed - Opened by JoepVanlier 9 months ago

#623 - kymo: crop beads out of kymograph

Pull Request - State: closed - Opened by JoepVanlier 9 months ago

#622 - Merge bug fixes from `1.3` back into `main`

Pull Request - State: closed - Opened by JoepVanlier 9 months ago

#621 - group: forward `contains` dunder to `h5py`

Pull Request - State: closed - Opened by JoepVanlier 9 months ago

#620 - tiff: don't rely on deprecated API for resolution unit

Pull Request - State: closed - Opened by JoepVanlier 9 months ago

#619 - merge `release` branch into `main`

Pull Request - State: closed - Opened by JoepVanlier 10 months ago

#618 - imagestack: fix adjustment single channel images

Pull Request - State: closed - Opened by JoepVanlier 10 months ago

#617 - ci: fix tests for `pytest>=8.0.0`

Pull Request - State: closed - Opened by JoepVanlier 10 months ago

#616 - docs: fix logo on pypi

Pull Request - State: closed - Opened by JoepVanlier 10 months ago

#615 - ImageStack: allow closing `ImageStack` file handles

Pull Request - State: closed - Opened by JoepVanlier 10 months ago

#614 - Move duplicated GMM/HMM properties to mixin

Pull Request - State: closed - Opened by rpauszek 10 months ago

#613 - force_calibration: fix small mistake in the documentation

Pull Request - State: closed - Opened by JoepVanlier 10 months ago

#612 - `ImageStack`: Make `include_dead_time=False` actually exclude the dead time.

Pull Request - State: closed - Opened by JoepVanlier 11 months ago

#611 - merge `1.3` back to `main`

Pull Request - State: closed - Opened by JoepVanlier 11 months ago

#610 - docs: fix import issue and add `id` field to notebook export

Pull Request - State: closed - Opened by JoepVanlier 11 months ago

#609 - plot_correlated: fix off by one error

Pull Request - State: closed - Opened by JoepVanlier 11 months ago - 3 comments

#608 - Fixup GMM API

Pull Request - State: closed - Opened by rpauszek 11 months ago

#607 - release_proc: merge bugfix back into main

Pull Request - State: closed - Opened by JoepVanlier 11 months ago

#606 - release: release pylake `1.3.1`

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

#605 - stack_roi.export_video with channel_slice does not produce a valid video

Issue - State: closed - Opened by ajasja 12 months ago - 3 comments

GitHub / lumicks/pylake issues and pull requests