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CHANGELOG.md

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## 1.5.0
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As this is a major release, not all changes and functions are listed below. For detailed information, please refer to the updated API documentation.
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As this is a major release, not all changes and functions are listed below. For
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detailed information, please refer to the updated API documentation.
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### Added
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* Various additions to `imcflibs.imagej.misc`:
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* `imcflibs.imagej.misc.send_notification_email` to send email notifications upon completion of long-running scripts.
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* Sends a mail with job details, such as recipient, file name, execution time & an optional message.
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* To enable email notifications, the following preferences must be set in `~/.imagej/IJ_Prefs.txt`:
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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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`~/.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, method logs a message and exits.
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* If the sender email or SMTP server is not configured, method logs a
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message and exits.
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* `imcflibs.imagej.misc.sanitize_image_title` to remove special chars and
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various suffixes from an ImagePlus.
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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 selected image windows.
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* `imcflibs.imagej.misc.get_threshold_value_from_method` to get the value that a selected AutoThreshold method would be using.
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* `imcflibs.imagej.misc.write_orderddict_to_csv` to write data from an ordered dictionary to a CSV file.
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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.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.
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* `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.
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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_orderddict_to_csv` to write data from an ordered
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dictionary to a CSV file.
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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.misc.save_image_in_format` to save an ImagePlus image in a
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specified format, such as ImageJ-TIF or OME-TIFF etc., to a given directory.
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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. Method uses
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`imcflibs.imagej.misc.locate_latest_imaris` to find the path to the Imaris
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installation.
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* New `imcflibs.imagej.objects3d` submodule, providing:
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* `imcflibs.imagej.objects3d.population3d_to_imgplus` to turn
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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 Dataset"
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command.
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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 `imcflibs.imagej.trackmate` submodule to provide helper functions to interface with Trackmate:
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* Multiple functions to set up Trackmate settings with different detectors, such as `cellpose`, `StarDist` or a `sparseLAP tracker`.
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* `imcflibs.imagej.trackmate.spot_filtering` to create settings to filter detected spots based on optional thresholds for quality, area, circularity & intensity.

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