Releases: jungmannlab/picasso
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
v0.6.9
Picasso 0.6.9 is here.
Changelog
- Polygonal pick added to Render -> draw any shape to pick localizations
- Save pick properties saves pick region's area in nm^2
- 3D calibration .yaml file saves the number of frames in the movie and the step size
Notes
v0.6.8
Picasso 0.6.8 is here.
Changelog
- .tiff files can be loaded to Localize directly, although the support may be limitted
- Bug fix: 2D cluster centers area and convex hull are saved correctly
- Bug fix: rectangular picks
Notes
v0.6.7
Picasso 0.6.7 is here.
Changelog
- GUI modules display the Picasso version number in the title bar
- Added readthedocs requirements file (only for developers)
- No blur applied when padding in Picasso: Render (increases speed of rendering)
- Camera settings saved in the .yaml file after localization
- Picasso: Design has the speed optimized extension sequences (Strauss and Jungmann, Nature Methods, 2020)
- Change matplotlib backend for macOS (bug fix with some plots being unavailable)
- Build animation does not trigger antivirus, which could delete Picasso (one click installer only)
Notes
v0.6.5
Picasso 0.6.5 is here.
Changelog
Many bug fixes for the one-click-installer version:
- Fix save pick properties bug in Picasso Render GUI (one click installer)
- Fix render render properties bug in Picasso Render GUI (one click installer)
- Fix animation building in Picasso Render GUI (one click installer)
- Fix test clusterer HDBSCAN bug
- Fix .nd2 localized files info loading (full loader changed to unsafe loader)
Fix rare bug with pick similar zero division error
Notes
v0.6.4
Picasso 0.6.4 is here.
Changelog
- Fix RCC error in one click installer (in versions 0.6.1-3)
- Picasso runs on Python 3.10 (jump from Python 3.7-3.8)
- New installation instructions
- Dependencies updated, meaning that M1 should have no problems with old versions of SciPy, etc.
- Localize: arbitrary number of sensitivity categories
- Picasso Render legend displays larger font
- Picasso Render Test Clusterer displays info when no clusters found instead of throwing an error
- Calling clustering functions from
picasso.clustererdoes not require camera pixel size. Same applies for the corresponding functions in CMD. Only if 3D localizations are used, the pixel size must be provided. - HDBSCAN is installed by default since it is distributed within the new version of
scikit-learn 1.3.0 - Screenshot
.yamlfile contains the list of colors used in the current rendering - Render scale bar allows only integer values (i.e., no decimals)
- Localize .ims file fitting bug solve
- Measuring in 3D render window (Measure tool and scalebar) fixed (previous versions showed incorrect values)
- Localize GUI allows for numerical ROI input (Parameters dialog)
- Export current view in Render saves metadata; an extra image is saved with a scalebar
- Allow loading individual .tif files (same as prior to v0.4.11)
- Clustering using CMD requires the user to input camera pixel size (instead of asking for the input after the function call)
- RESI localizations have new column 'cluster_id'
- Bug fixes
Notes
v0.6.0
Picasso 0.6.0 is here.
Changelog
- RESI dialog added to Picasso Render, allowing for substatial boost in spatial resolution (to be published)
- Quantum efficiency of a camera is not used anymore to convert raw data into photons. This affects localization precision calculated, such that it is closer to the experimental value obtained using NeNA
- Localize CMD: new argument (-r, --roi) for specifying ROI
v0.5.7
Picasso 0.5.7 is here.
Changelog
- Render group information is faster (e.g., clustered data)
- Test Clusterer window (Render) has multiple updates, e.g., different projections, cluster centers display
- Cluster centers contain info about std in x,y and z
- If localization precision in z-axis is provided, it will be rendered when using
Individual localization precisionandIndividual localization precision (iso). NOTE: the column must be namedlpzand have the same units aslpxandlpy. - Number of CPU cores used in multiprocessing limited at 60
- Bug fixes
Notes
v0.5.6
Picasso 0.5.6 is here.
Changelog
- Cluster centers contains analogous columns to the ones generated before the 0.5.x releases
- Clearer readme (installation instructions)
- Numerous bug fixes (custom colormap, robust .nd2 reading, close file, etc
- One click installer should not require administrator permissions (due to antivirus protection)
Notes