v0.9.1

Picasso 0.9.1 is here

Changelog

Important updates:

• Picasso does not use numpy.recarray objects anymore. pandas.DataFrame are used instead. This applies to localizations, drift data, cluster centers, etc. This change may cause backward compatibility issues when using Picasso as a package (downloaded from PyPI).
• Updated other dependencies, most importantly, numpy is now in version 2
• Old setup files were replaced by pyproject.toml for building and packaging Picasso
• New option to save cluster areas/volumes in DBSCAN, HDBSCAN and SMLM clusterer using Otsu thresholding of rendered images
• Localize: ensure that 3D calibration is centered at z = 0; this guarantees the correct z scaling (magnification factor)
• Render: unfold groups was removed as it is contained within the square grid unfolding
• Render: new pick shape - square
• Render: synchronize groups across channels - removes localizations from groups that are not present in all channels, e.g., after filtering cluster centers by frame analysis, the cluster localizations corresponding to removed cluster centers are also removed
• Render: save pick properties extended to saving group properties, also qpaint index is saved
• SPINNA: improved saved fit results summary (see issue #560)

Small improvements:

• Black-based code formatting applied to all scripts
• Cleaned up code for adjusting the size of QWidgets
• Progress dialog shows remaining time estimate more accurately (ignores the offset due to, for example, multiprocessing startup time)
• Render: save pick/group properties saves qpaint index (1 / mean dark time)
• Render: clustering metadata saves fraction of rejected localizations
• Render: screenshot .yaml files can be dragged and dropped to load the display settings
• Render: DBSCAN clustering .yaml file saves min. number of localizations per cluster
• Render 3D: display adjusted after changing blur method
• Localize: localization precision formula for least-squares fitting was corrected to account for a diagonal covariance Gaussian (background term is affected); the function for localization precision was moved from picasso.postprocess to picasso.gausslq
• SPINNA: GUI single sim does not allow the sum of proportions to exceed 100% (see issue #560)
• SPINNA: save last opened folder added
• SPINNA: smaller font size in NND plot for better readability
• SPINNA: clean up progress dialog
• SPINNA: NN plotting is normalized to 1000 nm
• Simplify the API for picking similar in picasso.postprocess

Bug fixes:

• Render: unfold groups/picks (rectangular grid) fixed for nonconsecutive grouping (the grid might have had missing elements before)
• Render: apply drift from external file fixed
• Render: fix masking (issue #560)
• Render: fix loading camera pixel size from metadata (see issue #560)
• Render: saving picks separately fixed areas in the .yaml files
• Render: loading a new channel with rendering by property fixed
• Render: mouse events are ignored if no localizations are loaded
• Render 3D: remove measurement points fixed
• Render 3D: save rotated localizations fixed
• Render 3D: fixed ind. loc. prec.
• Render 3D: rendering an empty pick fixed
• Localize: user-friendly display of large numbers (for example, 1,052,102 instead of 1052102)
• Localize: fixed acquisition comment extraction from uManager .tif files
• SPINNA: fixed all the bugs related to masking and search space generation (see issue #560)
• SPINNA: save NND plot fixed (when no simulations were run)
• SPINNA: read camera pixel size from metadata fixed (if available)

Notes

‼️ If installed in 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.
⚠️ Windows Safety features and Windows Defender may ask multiple times for permission during the installation and download.