jungmannlab · rafalkowalewski1 · Oct 5, 2025 · Oct 1, 2025 · Oct 1, 2025 · Oct 1, 2025
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.8.7
+current_version = 0.8.8
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

diff --git a/changelog.rst b/changelog.rst
@@ -1,7 +1,13 @@
 Changelog
 =========
 
-Last change: 01-OCT-2025 CEST
+Last change: 05-OCT-2025 CEST
+
+0.8.8
+-----
+- 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
+- Other bug fixes and minor improvements
 
 0.8.5-7
 -------

diff --git a/distribution/picasso.iss b/distribution/picasso.iss
@@ -2,10 +2,10 @@
 AppName=Picasso
 AppPublisher=Jungmann Lab, Max Planck Institute of Biochemistry
 
-AppVersion=0.8.7
+AppVersion=0.8.8
 DefaultDirName={commonpf}\Picasso
 DefaultGroupName=Picasso
-OutputBaseFilename="Picasso-Windows-64bit-0.8.7"
+OutputBaseFilename="Picasso-Windows-64bit-0.8.8"
 ArchitecturesAllowed=x64
 ArchitecturesInstallIn64BitMode=x64
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -26,7 +26,7 @@
 # The short X.Y version
 version = ""
 # The full version, including alpha/beta/rc tags
-release = "0.8.7"
+release = "0.8.8"
 
 # -- General configuration ---------------------------------------------------
 

diff --git a/docs/files.rst b/docs/files.rst
@@ -45,7 +45,16 @@ HDF5 Pick Property Files
 
 When selecting ``File > Save pick properties`` in ``Picasso: Render``, the properties of picked regions are stored in an HDF5 file. Within the HDF5 file, the data table is stored in the path ``/groups``.
 Each row in the “groups” table corresponds to one picked region. For each localization property (see Table 1), two columns are generated in the ``groups`` table: the mean and standard deviation of the respective column over the localizations in a pick region. For example, if the localization table contains a column ``len``, the “groups” table will contain a column ``len_mean`` and ``len_std``.
-Furthermore, the following columns are included: ``group`` (the group identifier), ``n_events`` (the number of localizations in the region) and ``n_units`` (the number of units from a qPAINT measurement).
+
+Furthermore, the following columns are included: 
+
+- ``group``: the group identifier;
+- ``n_events``: the number of binding events in the region;
+- ``n_units``: the number of units from a qPAINT measurement;
+- ``len_cdf`` and ``dark_cdf``: estimates of mean bright and dark times, respectively, obtained by fitting the distributions to the CDF of the exponential distribution. Units: frames;
+- ``locs``: the number of localizations in the region;
+- ``len_mean`` and ``dark_mean``: mean bright and dark times, respectively, obtained by averaging over all binding events, rather than fitting to the CDF. Units: frames;
+- ``len_std`` and ``dark_std``: standard deviation of bright and dark times,respectively;
 
 YAML Metadata Files
 -------------------

diff --git a/docs/plugins.png b/docs/plugins.png
diff --git a/docs/plugins.rst b/docs/plugins.rst
@@ -36,10 +36,4 @@ If you cloned the GitHub repository, you can add plugins by following these step
 
 For developers
 --------------
-To create a plugin, you can use the template provided in ``picasso/plugin_template.py``, see below.
-
-.. image:: ../docs/plugins.png
-   :scale: 70 %
-   :alt: Plugins
-
-As an example, please see any of the plugins in the `GitHub repo <https://github.com/rafalkowalewski1/picasso_plugins>`_.
+To create a plugin, you can use the template provided in `picasso/plugin_template.py <https://github.com/jungmannlab/picasso/blob/master/plugin_template.py>`_. For more examples of Plugins, please see the `GitHub repo <https://github.com/rafalkowalewski1/picasso_plugins>`_.
diff --git a/docs/render.rst b/docs/render.rst
@@ -54,6 +54,8 @@ Picking of regions of interest
 7. (Optional) Statistics about each pick region can be saved by selecting ``File > Save pick properties``. The resulting HDF5 file is not a localization file. Instead, it holds a data set called ``groups`` in which the rows show statistical values for each pick region.
 8. (Optional) The picked positions and diameter itself can be saved by selecting ``File > Save pick regions``. Such saved pick information can also be loaded into ``Picasso: Render`` by selecting ``File > Load pick regions``.
 
+**NOTE**: Rectangular picks can be used to generate the projections of localizations onto the rectangle's axes. To do so, select rectangular picks and save picked localizations (``File > Save picked localizations``). The resulting ``hdf5`` files will contain columns ``x_pick_rot`` and ``y_pick_rot``, which are the projections of localizations onto and against the "drawing" axis of the rectangle, respectively.
+
 3D rotation window
 ------------------
 
@@ -391,11 +393,11 @@ Removes the group information when loading a dataset that contains group informa
 
 Unfold / Refold groups
 ^^^^^^^^^^^^^^^^^^^^^^
-Allows to "unfold" an average to display each structure individually in a line. Also works with picks.
+Allows to "unfold" an average to display each structure individually in a line.Note that the structures need to be grouped and processed with Picasso: Average beforehand.
 
 Unfold groups (square)
 ^^^^^^^^^^^^^^^^^^^^^^
-Arranges an average in a square so that each structure is displayed individually
+Arranges an average in a square so that each structure is displayed individually. This function does not require Picasso: Average beforehand. Instead, grouped or picked (circular picks) localizations are accepted.
 
 Link localizations
 ^^^^^^^^^^^^^^^^^^

diff --git a/docs/table01.csv b/docs/table01.csv
@@ -11,9 +11,12 @@ lpy ,"The localization precision in y direction, in camera pixels, as estimated
 net_gradient ,"The net gradient of this spot which is defined by the sum of gradient vector magnitudes within the fitting box, projected to the spot center. ",float 
 z,(Optional) The z coordinate fitted in 3D in nm. Please note the units are different for x and y coordinates.,float 
 d_zcalib,"(Optional) The value of the D function used for z fitting with astigmatism, see the supplement to Huang et al. 2008.",float 
-likelihood ,The log-likelihood of the fit. Only available for MLE fitting.,float 
-iterations ,The number of iterations of the fit procedure. Only available for MLE fitting.,long 
-group ,"(Optional) An identifier to assign multiple localizations to groups, for example by picking regions of interest .",long 
-len ,"(Optional) The length of the event, if localizations from consecutive frames have been linked.",long 
+likelihood ,(Optional) The log-likelihood of the fit. Only available for MLE fitting.,float 
+iterations ,(Optional) The number of iterations of the fit procedure. Only available for MLE fitting.,long 
+group ,"(Optional) An identifier to assign multiple localizations to groups, for example by picking regions of interest or clustering. ",long 
+group_input, "(Optional) Assigned after clustering if the input localizations had a “group” column. This allows to trace back which input group a clustered group originated from.",long
+len ,"(Optional) The length of the event in frames, if localizations from consecutive frames have been linked.",long 
 n ,"(Optional) The number of localizations in this event, if localizations from consecutive frames have been linked, potentially diverging from the “len” column due to a transient dark time tolerance.",long 
-photon_rate ,"(Optional) The mean number of photons per frame, if localizations from consecutive frames have been linked. The total number of photons is set in the “photons” column. ",float 
+photon_rate ,"(Optional) The mean number of photons per frame, if localizations from consecutive frames have been linked. The total number of photons is set in the “photons” column. ",float 
+x_pick_rot ,"(Optional) Projection of localizations onto the axis of the rectangular pick. Only available after saving rectangular pick(s). ",float
+y_pick_rot ,"(Optional) Projection of localizations against the axis of the rectangular pick. Only available after saving rectangular pick(s). ",float
diff --git a/picasso/__init__.py b/picasso/__init__.py
@@ -11,7 +11,7 @@
 import os.path
 import yaml as yaml
 
-__version__ = "0.8.7"
+__version__ = "0.8.8"
 
 _this_file = os.path.abspath(__file__)
 _this_dir = os.path.dirname(_this_file)

diff --git a/picasso/__main__.py b/picasso/__main__.py
@@ -1539,7 +1539,10 @@ def _spinna_batch_analysis(
             locs, info = io.load_locs(str(row[f"exp_data_{target}"]))
             pixelsize = 130
             for element in info:
-                if "Picasso Localize" in element.values():
+                if (
+                    "Picasso" in element.values()
+                    and "Localize" in element.values()
+                ):  # in newer versions it's Picasso vX.Y.Z Localize
                     if "Pixelsize" in element:
                         pixelsize = element["Pixelsize"]
                         break

diff --git a/picasso/__version__.py b/picasso/__version__.py
@@ -1 +1 @@
-VERSION_NO = "0.8.7"
+VERSION_NO = "0.8.8"
diff --git a/picasso/gui/average.py b/picasso/gui/average.py
@@ -474,6 +474,7 @@ def set_image(self, image: np.ndarray) -> None:
         self._bgra[..., 0] = cmap[:, 2][image]
         self._bgra[..., 1] = cmap[:, 1][image]
         self._bgra[..., 2] = cmap[:, 0][image]
+        self._bgra[..., 3] = 255
         qimage = QtGui.QImage(self._bgra.data, X, Y, QtGui.QImage.Format_RGB32)
         self._pixmap = QtGui.QPixmap.fromImage(qimage)
         self.set_pixmap(self._pixmap)
@@ -541,6 +542,7 @@ def __init__(self) -> None:
         average_action = process_menu.addAction("Average")
         average_action.setShortcut("Ctrl+A")
         average_action.triggered.connect(self.view.average)
+        self.plugin_menu = menu_bar.addMenu("Plugins")  # do not delete
 
     def open(self) -> None:
         """Open the dialog for opening a file to load."""

diff --git a/picasso/gui/design.py b/picasso/gui/design.py
@@ -1789,6 +1789,9 @@ def initUI(self):
         palette.setColor(QtGui.QPalette.Background, QtCore.Qt.white)
         self.setPalette(palette)
 
+        menu_bar = QtWidgets.QMenuBar(self)
+        self.plugin_menu = menu_bar.addMenu("Plugins")  # do not delete
+
 
 def main():
     app = QtWidgets.QApplication(sys.argv)

diff --git a/picasso/gui/filter.py b/picasso/gui/filter.py
@@ -539,6 +539,8 @@ def __init__(self) -> None:
             pwd = []
         self.pwd = pwd
 
+        self.plugin_menu = menu_bar.addMenu("Plugins")  # do not delete
+
     def open_file_dialog(self) -> None:
         if self.pwd == []:
             path, exe = QtWidgets.QFileDialog.getOpenFileName(

diff --git a/picasso/gui/localize.py b/picasso/gui/localize.py
@@ -1510,6 +1510,8 @@ def init_menu_bar(self) -> None:
         calibrate_z_action = threed_menu.addAction("Calibrate 3D")
         calibrate_z_action.triggered.connect(self.calibrate_z)
 
+        self.plugin_menu = menu_bar.addMenu("Plugins")  # do not delete
+
     @property
     def camera_info(self) -> dict[str, float]:
         """Camera information, baseline, EM gain, sensitivity and QE."""

diff --git a/picasso/gui/nanotron.py b/picasso/gui/nanotron.py
@@ -1162,6 +1162,8 @@ def __init__(self, parent=None):
         mainWidget.setLayout(self.grid)
         self.setCentralWidget(mainWidget)
 
+        self.plugin_menu = menu_bar.addMenu("Plugins")  # do not delete
+
     def predict(self):
 
         if (self.predicting is False) and (self.model_loaded is True):