Merge pull request #249 from jungmannlab/0.4.2

0.4.2

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.1
+current_version = 0.4.2
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?
@@ -13,6 +13,12 @@ serialize =
 
 [bumpversion:file:./distribution/picasso.iss]
 
+[bumpversion:file:./picasso/__version__.py]
+
+[bumpversion:file:./release/one_click_windows_gui/picasso_innoinstaller.iss]
+
+[bumpversion:file:./release/one_click_windows_gui/create_installer_windows.bat]
+
 [bumpversion:file:setup.py]
 search = {current_version}
 replace = {new_version}

Dockerfile

@@ -0,0 +1,12 @@
+FROM ubuntu:20.04
+
+RUN apt-get update && apt-get install build-essential -y
+RUN apt-get install python3-pip -y
+
+WORKDIR /home/picasso/
+
+COPY . .
+
+RUN pip install .
+
+CMD ["bash"]

changelog.rst

@@ -1,9 +1,17 @@
 Changelog
 =========
 
-Last change: 23-MAR-2022 MTS
+Last change: 01-JUL-2022 MTS
 
-0.4.0
+0.4.2
+-----
+- 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
 

distribution/create_installer.bat

@@ -7,6 +7,8 @@ call conda create -n picasso_installer python=3.8 -y
 call conda activate picasso_installer
 call pip install pyinstaller==4.2
 cd %~dp0\..
+call DEL /F/Q/S dist > NUL
+call RMDIR /Q/S dist
 call pip install -r requirements.txt
 call python setup.py install
 cd %~dp0

distribution/picasso.iss

@@ -1,10 +1,10 @@
 [Setup]
 AppName=Picasso
 AppPublisher=Jungmann Lab, Max Planck Institute of Biochemistry
-AppVersion=0.4.1
+AppVersion=0.4.2
 DefaultDirName={pf}\Picasso
 DefaultGroupName=Picasso
-OutputBaseFilename="Picasso-Windows-64bit-0.4.1"
+OutputBaseFilename="Picasso-Windows-64bit-0.4.2"
 ArchitecturesAllowed=x64
 ArchitecturesInstallIn64BitMode=x64
 

docs/localize.rst

@@ -14,7 +14,7 @@ Localize allows performing super-resolution reconstruction of image stacks. For
 Identification and fitting of single-molecule spots
 ---------------------------------------------------
 
-1. In ``Picasso: Localize``, open a movie file by dragging the file into the window or by selecting ``File`` > ``Open``. If the movie is split into multiple μManager .tif files, open only the first file. Picasso will automatically detect the remaining files according to their file names. When opening a .raw file, a dialog will appear for file specifications.
+1. In ``Picasso: Localize``, open a movie file by dragging the file into the window or by selecting ``File`` > ``Open movie``. If the movie is split into multiple μManager .tif files, open only the first file. Picasso will automatically detect the remaining files according to their file names. When opening a .raw file, a dialog will appear for file specifications. When opening an IMS file it should be displayed immediately in the localize window. When opening an IMS file with multiple channels, a dialog window will appear allowing you to select the channel that should be loaded. You can navigate through the file using the arrow keys on your keyboard. The current frame is displayed in the lower right corner.
 2. Adjust the image contrast (select ``View`` > ``Contrast``) so that the single-molecule spots are clearly visible.
 3. To adjust spot identification and fit parameters, open the ``Parameters`` dialog (select ``Analyze`` > ``Parameters``).
 4. In the ``Identification`` group, set the ``Box side length`` to the rounded integer value of 6 × σ + 1, where σ is the standard deviation of the PSF. In an optimized microscope setup, σ is one pixel, and the respective ``Box side length`` should be set to 7. The value of ``Min. net gradient`` specifies a minimum threshold above which spots should be considered for fitting. The net gradient value of a spot is roughly proportional to its intensity, independent of its local background. By checking ``Preview``, the spots identified with the current settings will be marked in the displayed frame. Adjust ``Min. net gradient`` to a value at which only spots are detected (no background).

docs/render.rst

@@ -143,6 +143,13 @@ Load pick regions
 ^^^^^^^^^^^^^^^^^
 Resets the current picked regions and loads regions from a .yaml file that contains pick regions.
 
+Export ROI for Imaris
+^^^^^^^^^^^^^^^^^^^^^
+This function allows to export the current ROI for Imaris. Note that this is currently only implemented for Windows.
+Click on File / Export ROI for imaris and enter a filename for export. Picasso will export the current region of interest with the current oversampling settings. If multiple channels are loaded it will export the channels with the same colors as set in Picasso (Shortcut CTRL+F or View / Files to change.)
+Depending on the size of the ROI, the export will take a couple of seconds. Once exporting is finished, the file will be saved at the set location.
+The resulting file can be opened e.g. with ImarisViewer or Imaris. Note that the orientation is the same as in Picasso.
+
 Export localizations
 ^^^^^^^^^^^^^^^^^^^^
 Select export for various other programs. Note that some exporters only work for 3D files (with z coordinates). For additional file converters check out the convert folder at Picasso's GitHub page.
@@ -169,10 +176,6 @@ Export as .txt for FRC
 ++++++++++++++++++++++
 Export as .txt file to be used for the fourier ring correlation plugin in ImageJ.
 
-Export as .txt for IMARIS
-+++++++++++++++++++++++++
-Export as .txt file to be used for IMARIS import.
-
 Export as .xyz for Chimera
 ++++++++++++++++++++++++++
 Export as .txt file to be used for Chimera import.

picasso/__main__.py

@@ -934,16 +934,26 @@ def prompt_info():
             out_path = base + "_locs.hdf5"
             save_locs(out_path, locs, info)
             print("File saved to {}".format(out_path))
-            if args.drift > 0:
-                print("Undrifting file:")
-                print("------------------------------------------")
-                try:
-                    _undrift(
-                        out_path, args.drift, display=False, fromfile=None
-                    )
-                except Exception as e:
-                    print(e)
-                    print("Drift correction failed for {}".format(out_path))
+
+            if hasattr(args, 'database'):
+                CHECK_DB = args.database
+            else:
+                CHECK_DB = False
+
+            if CHECK_DB:
+                print('Adding to DB')
+                add_file_to_db(path, args.drift)
+            else:
+                if args.drift > 0:
+                    print("Undrifting file:")
+                    print("------------------------------------------")
+                    try:
+                        _undrift(
+                            out_path, args.drift, display=False, fromfile=None
+                        )
+                    except Exception as e:
+                        print(e)
+                        print("Drift correction failed for {}".format(out_path))
 
             print("                                          ")
     else:
@@ -1376,6 +1386,12 @@ def main():
     localize_parser.add_argument(
         "-zc", "--zc", type=str, default='', help="Path to 3d calibration file (only 3d)"
     )
+    localize_parser.add_argument(
+        "-db",
+        "--database",
+        action="store_true",
+        help="do not add to database",
+    )
 
     # nneighbors
     nneighbor_parser = subparsers.add_parser(

picasso/__version__.py

@@ -1 +1 @@
-VERSION_NO = "0.4.1"
+VERSION_NO = "0.4.2"