Releases: jungmannlab/picasso
v0.8.8
Picasso 0.8.8 is here
Changelog
- Render - masking dialog changed - threshold methods implemented, histogram of values shown, real-time rendering and different dialog layout
- Render - unfolding groups works without the Picasso: Average step beforehand
- Render by property: fixed the conflicts due to multi-channel, only single-channel compatible
- Other bug fixes and minor improvements
Notes
Program Files, Render and Localize may not be available for non-administrator users. Therefore, we recommend installing Picasso outside of Program Files. The current default location is C:\Picasso.
v0.8.7
Picasso 0.8.7 is here
Changelog
- Sound notifications when long processes finish, see here
- Several dialogs in Render, Localize and Simulate are now scrollable (experimental)
- SPINNA fix automatic area detection from picked localizations
- Render add dependency
imageio[ffmpeg]for building animations - Render allow for loading pick regions by dropping a .yaml file onto the window
- Render improve zooming with mouse wheel (Ctrl/Cmd + wheel)
- Fast rendering automatically adjusts constrast
- Localize show scale bar function added
- Localize plotted ROI remains the same when zooming in/out and panning
- Localize Gauss MLE saves number of iterations and fit log-likelihood
- DBSCAN accepts min. no. of localizations per cluster
- Cluster center calculations calculate arithmetic mean, not weighted mean
- Other bug fixes and minor improvements
Notes
Program Files, some modules (Render and Localize) may not be available for non-administrator users. Therefore, we recommend installing Picasso outside of Program Files.
v0.8.4
Picasso 0.8.4 is here
Changelog
- SPINNA - easy fitting of labeling efficiency
- GUI docstrings added in all scripts; cleaned up docstrings in Picasso modules
- Render: pick size chosen in nm, not camera pixels
- Code clean up (flake8 compliant)
- Other bug fixes
Notes
Program Files, some modules (Render and Localize) may not be available for non-administrator users. Therefore, we recommend installing Picasso outside of Program Files.
v0.8.3
Picasso 0.8.3 is here
Changelog
- Design: fix export plates and pipetting schemes
- Design: set default biotin excess to 25 (previously set to 1)
- Render by property allows different colormaps
- Removed
lmfitdependency - Fix cluster centers bug from v0.8.2
Notes
Program Files, some modules (Render and Localize) may not be available for non-administrator users. Therefore, we recommend installing Picasso outside of Program Files.
v0.8.2
Picasso 0.8.2 is here
Changelog
- New module SPINNA for investigating oligormerization of proteins; DOI: 10.1038/s41467-025-59500-z
- NeNA bug fix - old values were (usually) too high by a ~sqrt(2)
- NeNA bug fix - less prone to fitting to local maximum leading to incorrect values
- Added docstrings and data types in all modules (
postprocess,simulate,render,nanotron,localize,lib,io,imageprocess,gaussmle,gausslq,design,clusterer,aim,avgroiandzfit) - NeNA plot - displays distances in nm
- Fiducial picking - filter out picks too few localizations (80% of the total acquisition time)
picasso csv2hdfuses pandas to read .csv files- Added n_events to cluster centers, i.e., number of binding events per cluster
- .yaml files contain Picasso version number for easier tracking
- Improved fiducial picking
- Fix one click installer issues for non-administrator users
- Render allows for saving picked localizations in a separate file for each pick
- Remaining time estimate in the progress dialog
- Fix garbage collection when openinging
.nd2files in Localize - Fix 3D rotation window for a polygon pick
- Render minimap - the zoom-in window is always visible
- Bug fixes and other cosmetic changes
Notes
Program Files, some modules (Render and Localize) may not be available for non-administrator users. Therefore, we recommend installing Picasso outside of Program Files.
v0.7.5
Picasso 0.7.5 is here
Changelog
- Automatic picking of fiducials added in Render:
Tools/Pick fiducials - Undrifting from picked moved from
picasso/gui/rendertopicasso/postprocess - Plugin docs update
- Filter histogram display fixed for datasets with low variance (bug fix)
- AIM undrifting works now if the first frames of localizations are filtered out (bug fix)
- 2D drift plot in Render inverts y axis to match the rendered localizations
- 3D animation fixed
- Other minor bug fixes
Notes
v0.7.4
Picasso 0.7.4 is here.
Changelog
- Picasso: Render - adjust the scale bar's size automatically based on the current FOV's width
- Picasso: Render - RESI dialog fixed, units in nm
- Picasso: Render - show drift in nm, not camera pixels
- Picasso: Render - masking localizations saves the mask area in its metadata
- Picasso: Render - export current view across channels in grayscale
- Picasso: Render - title bar displays only the names of the currently opened files
- CMD implementation of AIM undrifting, see
picasso aim -hin terminal - CMD localize saves camera information in the metadata file
- Other minor bug fixes
Notes
v0.7.3
Picasso 0.7.3 is here.
Changelog
- Solved critical bug from v0.7.2 -> Localize not working
- SMLM clusterer in picked regions deleted
- Show legend in Render property displayed rounded tick label values
- Pick circular area does not save the area for each pick in localization's metadata
- Other minor bug fixes
Notes
v0.7.0
Picasso 0.7.0 is here.
Changelog
- Adaptive Intersection Maximization (AIM, doi: 10.1038/s41592-022-01307-0) implemented
- Z fitting improved by setting bounds on fitted z values to avoid NaNs
- CMD clusterfile fixed
- Picasso: Render 3D, rectangular and polygonal pick fixed
- picasso.localize.localize fixed
- default MLE fitting uses different sx and sy (CMD only)
Notes
v0.6.11
Picasso 0.6.11 is here.
Changelog
- picasso.lib.merge_locs function can merge localizations from multiple files
- Mask dialog in Picasso: Render saves .png mask file
- Mask dialog in Picasso: Render allows to save .png with the blurred image
- Picasso: Localize - added the option to save the current view as a .png file
- Picasso: Render - functions related to picking moved to picasso.lib and picasso.postprocess
- Picasso: Render - saving picked localizations saves the area(s) of the picked region(s) in the metadata file (.yaml)
- Documentation on readthedocs works again
Notes