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Another attempt to improve changelog readability
Refers to imcf#34
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‎CHANGELOG.md‎

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@@ -9,163 +9,175 @@ detailed information, please refer to the updated API documentation.
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### Added
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* **New functions** in `imcflibs.imagej.misc`:
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* `imcflibs.imagej.misc.send_notification_email` to send email notifications
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#### New functions in `imcflibs.imagej.misc`
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* `imcflibs.imagej.misc.send_notification_email` to send email notifications
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upon completion of long-running scripts.
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* Sends a mail with job details, such as recipient, file name, execution
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time & an optional message.
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* To enable email notifications, the following preferences must be set in
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* Sends a mail with job details, such as recipient, file name, execution time
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& an optional message.
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* To enable email notifications, the following preferences must be set in
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`~/.imagej/IJ_Prefs.txt`:
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* `.imcf.sender_email`: sender's email address.
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* `.imcf.smtpserver`: the SMTP server used for sending emails.
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* If the sender email or SMTP server is not configured, the method logs a
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* `.imcf.sender_email`: sender's email address.
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* `.imcf.smtpserver`: the SMTP server used for sending emails.
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* If the sender email or SMTP server is not configured, the method logs a
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message and returns.
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* `imcflibs.imagej.misc.sanitize_image_title` to remove special chars and
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* `imcflibs.imagej.misc.sanitize_image_title` to remove special chars and
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various suffixes from an ImagePlus' window title.
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* `imcflibs.imagej.misc.subtract_images` to subtract an image from another.
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* `imcflibs.imagej.misc.close_images` for closing all ImagePluses from a list.
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* `imcflibs.imagej.misc.get_threshold_value_from_method` to get the value that
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a selected _AutoThreshold_ method would be using.
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* `imcflibs.imagej.misc.write_ordereddict_to_csv` to write data from an
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ordered dictionary (or list of ordered dictionaries) to a CSV file.
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* `imcflibs.imagej.misc.save_image_in_format` to save an ImagePlus in a
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* `imcflibs.imagej.misc.subtract_images` to subtract an image from another.
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* `imcflibs.imagej.misc.close_images` for closing all ImagePluses from a list.
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* `imcflibs.imagej.misc.get_threshold_value_from_method` to get the value that a
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selected _AutoThreshold_ method would be using.
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* `imcflibs.imagej.misc.write_ordereddict_to_csv` to write data from an ordered
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dictionary (or list of ordered dictionaries) to a CSV file.
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* `imcflibs.imagej.misc.save_image_in_format` to save an ImagePlus in a
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specified format, such as `ImageJ-TIF` or `OME-TIFF` etc.
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* `imcflibs.imagej.misc.run_imarisconvert` to convert a given file to Imaris
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* `imcflibs.imagej.misc.run_imarisconvert` to convert a given file to Imaris
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format using the utility _ImarisConvert_. The function uses
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`imcflibs.imagej.misc.locate_latest_imaris` to find the path to the most
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recent Imaris installation.
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* **New functions** in `imcflibs.imagej.labelimage`:
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* `imcflibs.imagej.labelimage.cookie_cut_labels` to use a label image as a
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mask for another label image. Objects might get split or merged depending on
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the mask.
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* `imcflibs.imagej.labelimage.binary_to_label` for segmenting a binary image
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to get a label image (2D/3D).
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* `imcflibs.imagej.labelimage.relate_label_images` to relate two label images
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#### New functions in `imcflibs.imagej.labelimage`
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* `imcflibs.imagej.labelimage.cookie_cut_labels` to use a label image as a mask
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for another label image. Objects might get split or merged depending on the
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mask.
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* `imcflibs.imagej.labelimage.binary_to_label` for segmenting a binary image to
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get a label image (2D/3D).
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* `imcflibs.imagej.labelimage.relate_label_images` to relate two label images
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(2D/3D) using the _3D Association_ plugin from the 3DImageJSuite.
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* `imcflibs.imagej.labelimage.dilate_labels_2d` to dilate a label image slice
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by slice. Works for 2D or 3D images.
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* `imcflibs.imagej.labelimage.dilate_labels_2d` to dilate a label image slice by
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slice. Works for 2D or 3D images.
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#### New submodule `imcflibs.imagej.objects3d`
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* **New submodule** `imcflibs.imagej.objects3d`, providing:
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* `imcflibs.imagej.objects3d.population3d_to_imgplus` to turn an
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* `imcflibs.imagej.objects3d.population3d_to_imgplus` to turn an
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_Objects3DPopulation_ into an ImagePlus (2D/3D).
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* `imcflibs.imagej.objects3d.imgplus_to_population3d` to get the
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* `imcflibs.imagej.objects3d.imgplus_to_population3d` to get the
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_Objects3DPopulation_ from an ImagePlus (2D/3D).
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* `imcflibs.imagej.objects3d.segment_3d_image` to threshold an image into a
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* `imcflibs.imagej.objects3d.segment_3d_image` to threshold an image into a
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labeled stack.
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* `imcflibs.imagej.objects3d.get_objects_within_intensity` to filter a
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* `imcflibs.imagej.objects3d.get_objects_within_intensity` to filter a
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population of 3D objects by intensity.
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* `imcflibs.imagej.objects3d.maxima_finder_3d` to find local maxima in a
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3D image.
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* `imcflibs.imagej.objects3d.seeded_watershed` to perform a seeded watershed
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* `imcflibs.imagej.objects3d.maxima_finder_3d` to find local maxima in a 3D
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image.
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* `imcflibs.imagej.objects3d.seeded_watershed` to perform a seeded watershed
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segmentation on a binary image using seeds points.
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* **New submodule** `imcflibs.imagej.bdv`, providing _BigDataViewer_ related
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functionality:
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* Option configuration classes:
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* `imcflibs.imagej.bdv.ProcessingOptions` to configure the options on how
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the dataset should be processed
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* `imcflibs.imagej.bdv.DefinitionOptions` to hold the options on how a
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dataset is defined.
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* `imcflibs.imagej.bdv.check_processing_input` to sanitize and clarify the
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#### New submodule `imcflibs.imagej.bdv`
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Providing _BigDataViewer_ related functionality.
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* Option configuration classes:
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* `imcflibs.imagej.bdv.ProcessingOptions` to configure the options on how the
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dataset should be processed
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* `imcflibs.imagej.bdv.DefinitionOptions` to hold the options on how a dataset
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is defined.
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* `imcflibs.imagej.bdv.check_processing_input` to sanitize and clarify the
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`acitt` input selection.
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* `imcflibs.imagej.bdv.get_processing_settings` to generate the strings needed
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* `imcflibs.imagej.bdv.get_processing_settings` to generate the strings needed
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for the processing.
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* `imcflibs.imagej.bdv.backup_xml_files` to create a backup of BDV-XML files.
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* `imcflibs.imagej.bdv.define_dataset_auto` to run "_Define Multi-View
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Dataset_" using the "_Auto-Loader_" option.
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* `imcflibs.imagej.bdv.define_dataset_manual` to run "_Define Multi-View
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* `imcflibs.imagej.bdv.backup_xml_files` to create a backup of BDV-XML files.
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* `imcflibs.imagej.bdv.define_dataset_auto` to run "_Define Multi-View Dataset_"
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using the "_Auto-Loader_" option.
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* `imcflibs.imagej.bdv.define_dataset_manual` to run "_Define Multi-View
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Dataset_" using the "_Manual Loader_" option.
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* `imcflibs.imagej.bdv.resave_as_h5` to resave the dataset in H5 to make it
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* `imcflibs.imagej.bdv.resave_as_h5` to resave the dataset in H5 to make it
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compatible with BigDataViewer/BigStitcher.
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* `imcflibs.imagej.bdv.flip_axes` to call BigStitcher's "_Flip Axes_" command.
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* `imcflibs.imagej.bdv.phase_correlation_pairwise_shifts_calculation` to
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* `imcflibs.imagej.bdv.flip_axes` to call BigStitcher's "_Flip Axes_" command.
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* `imcflibs.imagej.bdv.phase_correlation_pairwise_shifts_calculation` to
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calculate pairwise shifts using Phase Correlation.
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* `imcflibs.imagej.bdv.filter_pairwise_shifts` for filtering pairwise shifts
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* `imcflibs.imagej.bdv.filter_pairwise_shifts` for filtering pairwise shifts
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based on different thresholds.
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* `imcflibs.imagej.bdv.optimize_and_apply_shifts` to optimize shifts and apply
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* `imcflibs.imagej.bdv.optimize_and_apply_shifts` to optimize shifts and apply
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them to a dataset.
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* `imcflibs.imagej.bdv.detect_interest_points` for running the "_Detect
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Interest Points_" command for registration.
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* `imcflibs.imagej.bdv.interest_points_registration` to run the "_Register
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* `imcflibs.imagej.bdv.detect_interest_points` for running the "_Detect Interest
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Points_" command for registration.
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* `imcflibs.imagej.bdv.interest_points_registration` to run the "_Register
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Dataset based on Interest Points_" command.
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* `imcflibs.imagej.bdv.duplicate_transformations` for duplicating /
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propagating transformation parameters to other channels.
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* `imcflibs.imagej.bdv.fuse_dataset` to call BigStitcher's "_Fuse Multi-View
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* `imcflibs.imagej.bdv.duplicate_transformations` for duplicating / propagating
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transformation parameters to other channels.
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* `imcflibs.imagej.bdv.fuse_dataset` to call BigStitcher's "_Fuse Multi-View
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Dataset_" command.
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* **New submodule** `imcflibs.imagej.trackmate` to provide helper functions to
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interface with _Trackmate_:
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* Multiple functions to set up Trackmate settings with different detectors:
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* `imcflibs.imagej.trackmate.cellpose_detector`
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* `imcflibs.imagej.trackmate.stardist_detector`
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* `imcflibs.imagej.trackmate.log_detector`
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* `imcflibs.imagej.trackmate.spot_filtering` to create settings to filter
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#### New submodule `imcflibs.imagej.trackmate`
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Providing helper functions to interface with _Trackmate_.
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* Multiple functions to set up Trackmate settings with different detectors:
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* `imcflibs.imagej.trackmate.cellpose_detector`
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* `imcflibs.imagej.trackmate.stardist_detector`
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* `imcflibs.imagej.trackmate.log_detector`
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* `imcflibs.imagej.trackmate.spot_filtering` to create settings to filter
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detected spots based on optional thresholds for quality, area, circularity &
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intensity.
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* `imcflibs.imagej.trackmate.sparse_lap_tracker` to create default settings
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for the sparse LAP tracker.
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* `imcflibs.imagej.trackmate.track_filtering` to create settings to filter
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* `imcflibs.imagej.trackmate.sparse_lap_tracker` to create default settings for
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the sparse LAP tracker.
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* `imcflibs.imagej.trackmate.track_filtering` to create settings to filter
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detected tracks based upon optional distances, such as `maximum linking`,
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`gap closing`, `track splitting & merging` and `maximum frame gap`.
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* `imcflibs.imagej.trackmate.run_trackmate` to run Trackmate with given
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settings (which can be set up with the methods in the
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`imcflibs.imagej.trackmate` submodule) to create a label image.
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* **New submodule** `imcflibs.imagej.omerotools`, providing helper functions to
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connect to _OMERO_ using user credentials, fetch and upload an image, retrieve
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a dataset or save ROIs to OMERO.
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* `imcflibs.imagej.omerotools.parse_url` to parse the OMERO URL and get a list
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* `imcflibs.imagej.trackmate.run_trackmate` to run Trackmate with given settings
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(which can be set up with the methods in the `imcflibs.imagej.trackmate`
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submodule) to create a label image.
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#### New submodule `imcflibs.imagej.omerotools`
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Providing helper functions to connect to _OMERO_ using user credentials, fetch
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and upload images, retrieve datasets or save ROIs to OMERO.
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* `imcflibs.imagej.omerotools.parse_url` to parse the OMERO URL and get a list
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of `ImageWrappers` from multiple image or datasets IDs.
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* `imcflibs.imagej.omerotools.connect` to connect to OMERO using user
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* `imcflibs.imagej.omerotools.connect` to connect to OMERO using user
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credentials.
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* `imcflibs.imagej.omerotools.fetch_image` to fetch an image from OMERO using
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* `imcflibs.imagej.omerotools.fetch_image` to fetch an image from OMERO using
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the image ID.
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* `imcflibs.imagej.omerotools.upload_image_to_omero` to upload a local image
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to OMERO and returning the new image ID.
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* `imcflibs.imagej.omerotools.add_keyvalue_annotation` to add an annotation to
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* `imcflibs.imagej.omerotools.upload_image_to_omero` to upload a local image to
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OMERO and returning the new image ID.
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* `imcflibs.imagej.omerotools.add_keyvalue_annotation` to add an annotation to
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an OMERO object.
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* `imcflibs.imagej.omerotools.delete_keyvalue_annotations` to delete key/value
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* `imcflibs.imagej.omerotools.delete_keyvalue_annotations` to delete key/value
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annotations from an OMERO object.
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* `imcflibs.imagej.omerotools.find_dataset` to find a dataset in OMERO using
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the dataset ID.
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* `imcflibs.imagej.get_acquisition_metadata` to get the acquisition metadata
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* `imcflibs.imagej.omerotools.find_dataset` to find a dataset in OMERO using the
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dataset ID.
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* `imcflibs.imagej.get_acquisition_metadata` to get the acquisition metadata
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from an image in OMERO.
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* `imcflibs.imagej.omerotools.get_info_from_original_metadata` to get the
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* `imcflibs.imagej.omerotools.get_info_from_original_metadata` to get the
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original metadata from an image in OMERO.
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* `imcflibs.imagej.omerotools.create_table_columns` to create OMERO table
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* `imcflibs.imagej.omerotools.create_table_columns` to create OMERO table
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headings from a list of column names.
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* `imcflibs.imagej.omerotools.upload_array_as_omero_table` to upload a table
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to OMERO.
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* `imcflibs.imagej.omerotools.save_rois_to_omero` to save ROIs to OMERO.
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* `imcflibs.imagej.omerotools.upload_array_as_omero_table` to upload a table to
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OMERO.
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* `imcflibs.imagej.omerotools.save_rois_to_omero` to save ROIs to OMERO.
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* **New submodule** `imcflibs.imagej.shading` for illumination correction:
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* `imcflibs.imagej.shading.simple_flatfield_correction` to perform a
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simple flatfield correction to an ImagePlus.
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#### New submodule `imcflibs.imagej.shading`
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* **New submodule** `imcflibs.imagej.processing` containing utilities for
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filtering and thresholding:
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* `imcflibs.imagej.processing.apply_filter` to apply a filter to an
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ImagePlus.
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* `imcflibs.imagej.processing.apply_rollingball_bg_subtraction` to apply a
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* `imcflibs.imagej.shading.simple_flatfield_correction` to perform a simple
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flatfield correction to an ImagePlus.
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#### New submodule `imcflibs.imagej.processing`
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Utilities for filtering and thresholding.
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* `imcflibs.imagej.processing.apply_filter` to apply a filter to an ImagePlus.
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* `imcflibs.imagej.processing.apply_rollingball_bg_subtraction` to apply a
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rolling ball background subtraction to an ImagePlus.
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* `imcflibs.imagej.processing.apply_threshold` to apply a threshold method to
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an ImagePlus.
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* `imcflibs.imagej.processing.apply_threshold` to apply a threshold method to an
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ImagePlus.
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* **New functions** in `imcflibs.imagej.bioformats`:
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* `imcflibs.imagej.bioformats.export` to export an image to a given file.
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* `imcflibs.imagej.bioformats.get_metadata_from_file` to extract various
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#### New functions in `imcflibs.imagej.bioformats`
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* `imcflibs.imagej.bioformats.export` to export an image to a given file.
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* `imcflibs.imagej.bioformats.get_metadata_from_file` to extract various
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metadata from a given file using BioFormats.
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* `imcflibs.imagej.bioformats.get_stage_coords`to get stage coordinates and
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* `imcflibs.imagej.bioformats.get_stage_coords`to get stage coordinates and
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calibration for one or more given images.
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#### Other new functions
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* `imcflibs.strtools.pad_number` to pad a number with leading zeros.
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* `imcflibs.pathtools.create_directory` to create a new directory at the
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specified path if it does not exist (needed for Python 2.7).
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* `imcflibs.imagej.prefs.set_default_ij_options` to configure ImageJ default
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options to ensure consistent behavior.
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* `imcflibs.imagej.projections.project_stack` to project a stack along a defined
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axis using one of the available projection methods, such as `max`, `min`,
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`mean`, `sum` or `standard_deviation`.

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