Minor changes to improve readability

Refers to imcf#34

Author: ehrenfeu

CHANGELOG.md

@@ -11,8 +11,9 @@ detailed information, please refer to the updated API documentation.
 
 * `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 with python 2.7)
-* Various additions to `imcflibs.imagej.misc`:
+  specified path if it does not exist (needed for Python 2.7).
+
+* **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
@@ -24,34 +25,36 @@ detailed information, please refer to the updated API documentation.
     * 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.
+    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.
+    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., to a given directory.
+    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. Method uses
-    `imcflibs.imagej.misc.locate_latest_imaris` to find the path to the Imaris
-    installation.
-* New functions in `imcflibs.imagej.labelimage`:
+    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.
+    (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 `imcflibs.imagej.objects3d` submodule, providing:
+
+* **New submodule** `imcflibs.imagej.objects3d`, providing:
   * `imcflibs.imagej.objects3d.population3d_to_imgplus` to turn an
-    Objects3DPopulation into an ImagePlus (2D/3D).
+    _Objects3DPopulation_ into an ImagePlus (2D/3D).
   * `imcflibs.imagej.objects3d.imgplus_to_population3d` to get the
-    Objects3DPopulation from an ImagePlus (2D/3D).
+    _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
@@ -60,60 +63,62 @@ detailed information, please refer to the updated API documentation.
     3D image.
   * `imcflibs.imagej.objects3d.seeded_watershed` to perform a seeded watershed
     segmentation on a binary image using seeds points.
-* New `imcflibs.imagej.bdv` submodule, providing BigDataViewer related
-  functions:
-  * New classes:
-    * `imcflibs.imagej.bdv.ProcessingOptions` to store all options on how to
-      process the dataset.
-    * `imcflibs.imagej.bdv.DefinitionOptions` to store all options on how to
-      define the dataset.
+
+* **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.
+    `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.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.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.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 `imcflibs.imagej.trackmate` submodule to provide helper functions to
-  interface with Trackmate:
-  * Multiple functions to set up Trackmate settings with different detectors,
-    such as `imcflibs.imagej.trackmate.cellpose_detector`,
-    `imcflibs.imagej.trackmate.stardist_detector` or a
-    `imcflibs.imagej.trackmate.log_detector`.
+  * `imcflibs.imagej.bdv.fuse_dataset` to call BigStitcher's "_Fuse Multi-View
+    Dataset_" command.
+
+* **New submodule** `imcflibs.imagej.trackmate` to provide 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 Fiji's Trackmate plugin on
-    an open ImagePlus with given settings, which can be set up with available
-    methods in the `imcflibs.imagej.trackmate` submodule. The method then
-    returns a label image.
-* New `imcflibs.imagej.omerotools` submodule, providing helper functions to
-  connect to OMERO using user credentials, fetch and upload an image, retrieve a
-  dataset,  or save ROIs to OMERO.
+    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 an image, retrieve
+  a dataset 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
@@ -124,7 +129,7 @@ detailed information, please refer to the updated API documentation.
     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
+  * `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.
@@ -137,20 +142,24 @@ detailed information, please refer to the updated API documentation.
   * `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 `imcflibs.imagej.shading` module for everything background correction.
+
+* **New submodule** `imcflibs.imagej.shading` for illumination correction:
   * `imcflibs.imagej.shading.simple_flatfield_correction` to perform a
     simple flatfield correction to an ImagePlus.
+
 * `imcflibs.imagej.prefs.set_default_ij_options` to configure ImageJ default
-  options for consistency.
-* New module `imcflibs.imagej.processing` containing utilities for filtering and thresholding:
+  options to ensure consistent behavior.
+
+* **New submodule** `imcflibs.imagej.processing` containing 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.
 
-* Additions to `imcflibs.imagej.bioformats`:
+* **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.
@@ -235,7 +244,7 @@ detailed information, please refer to the updated API documentation.
 
 * 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`:
+  via ImageJ2's _Script Parameter_ `@# File`:
   * `imcflibs.pathtools.parse_path`
   * `imcflibs.strtools.filename`
 * Several changes in `imcflibs.pathtools.parse_path`: