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Changelog

Last change: 14-DEC-2024 MTS

0.7.1 - 0.7.4

  • 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
  • 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 the file only the names of the currently opened files
  • CMD implementation of AIM undrifting, see picasso aim -h in terminal
  • CMD localize saves camera information in the metadata file
  • Other minor bug fixes

0.7.0

  • 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)

0.6.9 - 0.6.11

  • Added the option to draw polygon picks in Picasso: Render
  • Save pick properties in Picasso: Render saves areas of picked regions in nm^2
  • Calibration .yaml file saves number of frames and step size in nm
  • picasso.lib.merge_locs function can merge localizations from multiple files
  • Mask dialog in Picasso: Render saves .png mask files
  • 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

0.6.6 - 0.6.8

  • 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)
  • .tiff files can be loaded to Localize directly, although the support may limited!
  • Bug fix: build animation does not trigger antivirus, which could delete Picasso (one click installer only)
  • Bug fix: 2D cluster centers area and convex hull are saved correctly
  • Bug fix: rectangular picks

0.6.3 - 0.6.5

  • Dependencies updated
  • Bug fixes due to Python 3.10 and PyQt5 (listed below)
  • Fix RCC error for Render GUI (one click installer) (remove tqdm from GUI)
  • 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
  • Update installation instructions

0.6.2

  • 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.clusterer does 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 .yaml file 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

0.6.1

  • Measuring in the 3D window (Measure and Scalebar) fixed (previous versions did not convert the value correctly)
  • Localize GUI allows for numerical ROI input in the Parameters Dialog
  • Allow loading individual .tif files as in Picasso v0.4.11``
  • RESI localizations have the new column cluster_id
  • Building animation shows progress (Render 3D)
  • Export current view in Render saves metadata; An extra image is saved with a scalebar if the user did not set it
  • (Not applicable in 0.6.2) Clustering in command window requires camera pixel size to be input (instead of inserting one after calling the function)
  • Bug fixes

0.6.0

  • New RESI (Resolution Enhancement by Sequential Imaging) dialog in Picasso Render allowing for a substantial resolution boost, (Reinhardt, et al., Nature, 2023. DOI: 10.1038/s41586-023-05925-9)
  • Remove quantum efficiency when converting raw data into photons in Picasso Localize
  • Input ROI using command-line picasso localize, see here.

0.5.7

  • Updated installation instructions
  • (H)DBSCAN available from cmd (bug fix)
  • 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 precision and Individual localization precision (iso). NOTE: the column must be named lpz and have the same units as lpx and lpy.
  • Number of CPU cores used in multiprocessing limited at 60
  • Updated 3D rendering and clustering documentation
  • Bug fixes

0.5.5-6

  • Cluster info is saved in _cluster_centers.hdf5 files which are created when Save cluster centers box is ticked
  • Cluster centers contain info about group, mean frame (saved as frame), standard deviation frame, area/volume and convex hull
  • gist_rainbow is used for rendering properties
  • NeNA can be calculated many times
  • Bug fixes

0.5.1-4

  • Sensitivity is a float number in Server: Watcher
  • One-click-installer available
  • Bug fixes

0.5.0

  • 3D rendering rotation window
  • Multiple .hdf5 files can be loaded when using File->Open
  • Localizations can be combined when saving
  • Render window restart (Remove all localizations)
  • Multiple pyplot colormaps available in Render
  • View->Files in Render substantially changed (many new colors, close button works, etc)
  • Changing Render's FOV with W, A, S and D
  • Render's FOV can be numerically changed, saved and loaded in View->Info
  • Pick similar is much faster
  • Remove localization in picks
  • Fast rendering (display a fraction of localizations)
  • .txt file with drift can be applied to localizations in Render
  • New clustering algorithm (SMLM clusterer)
  • Test clusterer window in Render
  • Option to calculate cluster centers
  • Nearest neighbor analysis in Render
  • Numerical filter in Filter
  • New file format in Localize - .nd2
  • Localize can read NDTiffStack.tif files
  • Docstrings for Render
  • Plugins can be added to all Picasso modules
  • Many other improvements, bug fixes, etc.

0.4.6-10

  • Logging for Watcher of Picasso Server
  • Mode for multiple parameter groups for Watcher
  • Fix for installation on Mac systems
  • Various bugfixes

0.4.2-5

  • Added more docstrings / documentation for Picasso Server
  • Import and export for handling IMS (Imaris) files
  • Fixed a bug where GPUFit was greyed out, added better installation instructions for GPUfit
  • More documentation
  • Added dockerfile

0.4.1

  • Fixed a bug in installation

0.4.0

  • Added new module "Picasso Server"