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Add info about changes for BDV #72

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Add info about changes for BDV
lguerard Mar 31, 2025
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ehrenfeu Apr 8, 2025
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59 changes: 34 additions & 25 deletions CHANGELOG.md
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Expand Up @@ -4,34 +4,38 @@

## 1.5.0

As this is a major release, not all changes and functions are listed below. For detailed information, please refer to the updated API documentation.
As this is a major release, not all changes and functions are listed below. For
detailed information, please refer to the updated API documentation.

### Added

* Various additions to `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.
* `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, method logs a message and
exits.
* `imcflibs.imagej.misc.sanitize_image_title` to remove special chars and various
suffixes from an ImagePlus.
* If the sender email or SMTP server is not configured, method logs a
message and exits.
* `imcflibs.imagej.misc.sanitize_image_title` to remove special chars and
various suffixes from an ImagePlus.
* `imcflibs.imagej.misc.subtract_images` to subtract an image from another.
* `imcflibs.imagej.misc.close_images` for closing selected image windows.
* `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 to a CSV file.
* `imcflibs.imagej.labelimage.binary_to_label` for segmenting a binary image to get a
label image (2D/3D).
* `imcflibs.imagej.misc.save_image_in_format` to save an ImagePlus image in a specified
format, such as ImageJ-TIF or OME-TIFF etc., to a given directory.
* `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.
* `imcflibs.imagej.misc.get_threshold_value_from_method` to get the value that
a selected AutoThreshold method would be using.
* `imcflibs.imagej.misc.write_orderddict_to_csv` to write data from an ordered
dictionary to a CSV file.
* `imcflibs.imagej.labelimage.binary_to_label` for segmenting a binary image to
get a label image (2D/3D).
* `imcflibs.imagej.misc.save_image_in_format` to save an ImagePlus image in a
specified format, such as ImageJ-TIF or OME-TIFF etc., to a given directory.
* `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 `imcflibs.imagej.objects3d` submodule, providing:
* `imcflibs.imagej.objects3d.population3d_to_imgplus` to turn
Expand All @@ -44,13 +48,20 @@ As this is a major release, not all changes and functions are listed below. For
population of 3D objects by intensity.
* New `imcflibs.imagej.bdv` submodule, providing BigDataViewer related
functions:
* `imcflibs.imagej.bdv.backup_xml_files` to create a backup of BDV-XML files
* New classes:
* `ProcessingOptions` to store all options on how to process the dataset.
* `DefinitionOptions` to store all options on how to define the dataset.
* `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 xml dataset in a new format
(either all or single timepoints).
* `imcflibs.imagej.bdv.resave_as_h5` to resave the dataset in H5 to
make it compatible with BigDataViewer/BigStitcher.
* `imcflibs.imagej.bdv.flip_axes` tocall BigStitcher's "Flip Axes" command.
* `imcflibs.imagej.bdv.phase_correlation_pairwise_shifts_calculation` to
calculate pairwise shifts using Phase Correlation.
Expand All @@ -64,15 +75,13 @@ As this is a major release, not all changes and functions are listed below. For
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 Dataset"
command.

* `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 `cellpose`, `StarDist` or a `sparseLAP tracker`.
* `imcflibs.imagej.trackmate.spot_filtering` to create settings to filter detected spots based on optional thresholds for quality, area, circularity & intensity.
* `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.

* `imcflibs.pathtools.create_directory` to create a new directory at the specified path.
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