CHANGELOG.md

Changelog 🧾

1.5.0

This release brings a lot of additions, not all changes and functions are explained in depth below. For detailed information, please refer to the updated API documentation.

Added

New functions in imcflibs.imagej.misc

• imcflibs.imagej.misc.send_notification_email to send email notifications upon completion of long-running scripts.
  • Sends a mail with job details, such as recipient, file name, execution time & an optional message.
  • To enable email notifications, the following preferences must be set in ~/.imagej/IJ_Prefs.txt:
    • .imcf.sender_email: sender's email address.
    • .imcf.smtpserver: the SMTP server used for sending emails.
  • If the sender email or SMTP server is not configured, the method logs a message and returns.
• imcflibs.imagej.misc.sanitize_image_title to remove special chars and various suffixes from an ImagePlus' window title.
• imcflibs.imagej.misc.subtract_images to subtract an image from another.
• imcflibs.imagej.misc.close_images for closing all ImagePluses from a list.
• imcflibs.imagej.misc.get_threshold_value_from_method to get the value that a selected AutoThreshold method would be using.
• imcflibs.imagej.misc.write_ordereddict_to_csv to write data from an ordered dictionary (or list of ordered dictionaries) to a CSV file.
• imcflibs.imagej.misc.save_image_in_format to save an ImagePlus in a specified format, such as ImageJ-TIF or OME-TIFF etc.
• imcflibs.imagej.misc.run_imarisconvert to convert a given file to Imaris format using the utility ImarisConvert. The function uses imcflibs.imagej.misc.locate_latest_imaris to find the path to the most recent Imaris installation.

New functions in imcflibs.imagej.labelimage

• imcflibs.imagej.labelimage.cookie_cut_labels to use a label image as a mask for another label image. Objects might get split or merged depending on the mask.
• imcflibs.imagej.labelimage.binary_to_label for segmenting a binary image to get a label image (2D/3D).
• imcflibs.imagej.labelimage.relate_label_images to relate two label images (2D/3D) using the 3D Association plugin from the 3DImageJSuite.
• imcflibs.imagej.labelimage.dilate_labels_2d to dilate a label image slice by slice. Works for 2D or 3D images.

New submodule imcflibs.imagej.objects3d

• imcflibs.imagej.objects3d.population3d_to_imgplus to turn an Objects3DPopulation into an ImagePlus (2D/3D).
• imcflibs.imagej.objects3d.imgplus_to_population3d to get the Objects3DPopulation from an ImagePlus (2D/3D).
• imcflibs.imagej.objects3d.segment_3d_image to threshold an image into a labeled stack.
• imcflibs.imagej.objects3d.get_objects_within_intensity to filter a population of 3D objects by intensity.
• imcflibs.imagej.objects3d.maxima_finder_3d to find local maxima in a 3D image.
• imcflibs.imagej.objects3d.seeded_watershed to perform a seeded watershed segmentation on a binary image using seeds points.

New submodule imcflibs.imagej.bdv

Providing BigDataViewer related functionality.

• Option configuration classes:
  • imcflibs.imagej.bdv.ProcessingOptions to configure the options on how the dataset should be processed
  • imcflibs.imagej.bdv.DefinitionOptions to hold the options on how a dataset is defined.
• imcflibs.imagej.bdv.check_processing_input to sanitize and clarify the acitt input selection.
• imcflibs.imagej.bdv.get_processing_settings to generate the strings needed for the processing.
• imcflibs.imagej.bdv.backup_xml_files to create a backup of BDV-XML files.
• imcflibs.imagej.bdv.define_dataset_auto to run "Define Multi-View Dataset" using the "Auto-Loader" option.
• imcflibs.imagej.bdv.define_dataset_manual to run "Define Multi-View Dataset" using the "Manual Loader" option.
• imcflibs.imagej.bdv.resave_as_h5 to resave the dataset in H5 to make it compatible with BigDataViewer/BigStitcher.
• imcflibs.imagej.bdv.flip_axes to call BigStitcher's "Flip Axes" command.
• imcflibs.imagej.bdv.phase_correlation_pairwise_shifts_calculation to calculate pairwise shifts using Phase Correlation.
• imcflibs.imagej.bdv.filter_pairwise_shifts for filtering pairwise shifts based on different thresholds.
• imcflibs.imagej.bdv.optimize_and_apply_shifts to optimize shifts and apply them to a dataset.
• imcflibs.imagej.bdv.detect_interest_points for running the "Detect Interest Points" command for registration.
• imcflibs.imagej.bdv.interest_points_registration to run the "Register Dataset based on Interest Points" command.
• imcflibs.imagej.bdv.duplicate_transformations for duplicating / propagating transformation parameters to other channels.
• imcflibs.imagej.bdv.fuse_dataset to call BigStitcher's "Fuse Multi-View Dataset" command.

New submodule imcflibs.imagej.trackmate

Providing helper functions to interface with Trackmate.

• Multiple functions to set up Trackmate settings with different detectors:
  • imcflibs.imagej.trackmate.cellpose_detector
  • imcflibs.imagej.trackmate.stardist_detector
  • imcflibs.imagej.trackmate.log_detector
• imcflibs.imagej.trackmate.spot_filtering to create settings to filter detected spots based on optional thresholds for quality, area, circularity & intensity.
• imcflibs.imagej.trackmate.sparse_lap_tracker to create default settings for the sparse LAP tracker.
• imcflibs.imagej.trackmate.track_filtering to create settings to filter detected tracks based upon optional distances, such as maximum linking, gap closing, track splitting & merging and maximum frame gap.
• imcflibs.imagej.trackmate.run_trackmate to run Trackmate with given settings (which can be set up with the methods in the imcflibs.imagej.trackmate submodule) to create a label image.

New submodule imcflibs.imagej.omerotools

Providing helper functions to connect to OMERO using user credentials, fetch and upload images, retrieve datasets or save ROIs to OMERO.

• imcflibs.imagej.omerotools.parse_url to parse the OMERO URL and get a list of ImageWrappers from multiple image or datasets IDs.
• imcflibs.imagej.omerotools.connect to connect to OMERO using user credentials.
• imcflibs.imagej.omerotools.fetch_image to fetch an image from OMERO using the image ID.
• imcflibs.imagej.omerotools.upload_image_to_omero to upload a local image to OMERO and returning the new image ID.
• imcflibs.imagej.omerotools.add_keyvalue_annotation to add an annotation to an OMERO object.
• imcflibs.imagej.omerotools.delete_keyvalue_annotations to delete key/value annotations from an OMERO object.
• imcflibs.imagej.omerotools.find_dataset to find a dataset in OMERO using the dataset ID.
• imcflibs.imagej.omerotools.get_acquisition_metadata to get the acquisition metadata from an image in OMERO.
• imcflibs.imagej.omerotools.get_info_from_original_metadata to get the original metadata from an image in OMERO.
• imcflibs.imagej.omerotools.create_table_columns to create OMERO table headings from a list of column names.
• imcflibs.imagej.omerotools.upload_array_as_omero_table to upload a table to OMERO.
• imcflibs.imagej.omerotools.save_rois_to_omero to save ROIs to OMERO.

New submodule imcflibs.imagej.shading

• imcflibs.imagej.shading.simple_flatfield_correction to perform a simple flatfield correction to an ImagePlus.

New submodule imcflibs.imagej.processing

Utilities for filtering and thresholding.

• imcflibs.imagej.processing.apply_filter to apply a filter to an ImagePlus.
• imcflibs.imagej.processing.apply_rollingball_bg_subtraction to apply a rolling ball background subtraction to an ImagePlus.
• imcflibs.imagej.processing.apply_threshold to apply a threshold method to an ImagePlus.

New functions in imcflibs.imagej.bioformats

• imcflibs.imagej.bioformats.export to export an image to a given file.
• imcflibs.imagej.bioformats.get_metadata_from_file to extract various metadata from a given file using BioFormats.
• imcflibs.imagej.bioformats.get_stage_coordsto get stage coordinates and calibration for one or more given images.

Other new functions

• imcflibs.strtools.pad_number to pad a number with leading zeros.
• imcflibs.pathtools.create_directory to create a new directory at the specified path if it does not exist (needed for Python 2.7).
• imcflibs.imagej.prefs.set_default_ij_options to configure ImageJ default options to ensure consistent behavior.
• imcflibs.imagej.projections.project_stack to project a stack along a defined axis using one of the available projection methods, such as max, min, mean, sum or standard_deviation.

Changed

• imcflibs.pathtools.listdir_matching now has an additional optional boolean parameter regex to request the parameter suffix being interpreted as a regular expression for filtering.
• imcflibs.imagej.misc.calculate_mean_and_stdv now has an optional parameter round_decimals to allow for rounding the results, defaulting to 0.

1.4.0

Added

• imcflibs.strtools.sort_alphanumerically to sort a list of strings taking into account numerical values correctly.

Changed

• imcflibs.pathtools.listdir_matching is now using the new sort_alphanumerically() function from above.

1.3.0

Added

• New functions in imcflibs.pathtools:
  • imcflibs.pathtools.join2 can be used to join paths, much like os.path.join except that it will work with java.io.File objects as well (but doesn't support more than two path components / parameters).
  • imcflibs.pathtools.find_dirs_containing_filetype
  • imcflibs.pathtools.folder_size
• New functions in imcflibs.imagej.misc:
  • imcflibs.imagej.misc.calculate_mean_and_stdv
  • imcflibs.imagej.misc.elapsed_time_since
  • imcflibs.imagej.misc.find_focus
  • imcflibs.imagej.misc.get_free_memory
  • imcflibs.imagej.misc.percentage
  • imcflibs.imagej.misc.progressbar
  • imcflibs.imagej.misc.setup_clean_ij_environment
  • imcflibs.imagej.misc.timed_log
• New imcflibs.imagej.labelimage submodule, providing:
  • imcflibs.imagej.labelimage.filter_objects
  • imcflibs.imagej.labelimage.label_image_to_roi_list
  • imcflibs.imagej.labelimage.measure_objects_size_shape_2d
  • imcflibs.imagej.labelimage.relate_label_images
• New imcflibs.imagej.gpu submodule, providing:
  • imcflibs.imagej.gpu.erode_labels
  • imcflibs.imagej.gpu.dilate_labels
  • imcflibs.imagej.gpu.merge_labels
• New imcflibs.imagej.resultstable submodule, providing:
  • imcflibs.imagej.resultstable.add_results_to_resultstable
  • imcflibs.imagej.resultstable.get_resultstable
  • imcflibs.imagej.resultstable.preset_results_column
• New imcflibs.imagej.roimanager submodule, providing:
  • imcflibs.imagej.roimanager.add_rois_to_roimanager
  • imcflibs.imagej.roimanager.change_roi_color
  • imcflibs.imagej.roimanager.clear_ij_roi_manager
  • imcflibs.imagej.roimanager.count_all_rois
  • imcflibs.imagej.roimanager.enlarge_all_rois
  • imcflibs.imagej.roimanager.extract_color_of_all_rois
  • imcflibs.imagej.roimanager.get_roimanager
  • imcflibs.imagej.roimanager.load_rois_from_zip
  • imcflibs.imagej.roimanager.measure_in_all_rois
  • imcflibs.imagej.roimanager.rename_rois_by_number
  • imcflibs.imagej.roimanager.rename_rois
  • imcflibs.imagej.roimanager.save_rois_to_zip
  • imcflibs.imagej.roimanager.scale_all_rois
  • imcflibs.imagej.roimanager.select_rois_above_min_intensity
  • imcflibs.imagej.roimanager.shift_roi_by_bounding_box
  • imcflibs.imagej.roimanager.show_all_rois_on_image

Changed

• The functions below now also accept parameters of type java.io.File (instead of str), making them safe for being used directly with variables retrieved via ImageJ2's Script Parameter @# File:
  • imcflibs.pathtools.parse_path
  • imcflibs.strtools.filename
• Several changes in imcflibs.pathtools.parse_path:
  • The returned dict now contains an additional key basename that provides the filename without extension.
  • OME-TIFF filenames are now treated as special cases in the sense that the .ome part is stripped from the basename key and added to the ext key instead (as it is part of the suffix).
• imcflibs.pathtools.listdir_matching now has an additional optional argument sort (defaulting to False) to request the resulting list to be sorted.
• Many improvements / clarifications in function docstrings.