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4 | 4 |
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5 | 5 | ## 1.5.0 |
6 | 6 |
|
7 | | -As this is a major release, not all changes and functions are listed below. For detailed information, please refer to the updated API documentation. |
| 7 | +As this is a major release, not all changes and functions are listed below. For |
| 8 | +detailed information, please refer to the updated API documentation. |
8 | 9 |
|
9 | 10 | ### Added |
10 | 11 |
|
11 | 12 | * Various additions to `imcflibs.imagej.misc`: |
12 | | - * `imcflibs.imagej.misc.send_notification_email` to send email notifications upon completion of long-running scripts. |
13 | | - * Sends a mail with job details, such as recipient, file name, execution time & an optional message. |
14 | | - * To enable email notifications, the following preferences must be set in `~/.imagej/IJ_Prefs.txt`: |
| 13 | + * `imcflibs.imagej.misc.send_notification_email` to send email notifications |
| 14 | + upon completion of long-running scripts. |
| 15 | + * Sends a mail with job details, such as recipient, file name, execution |
| 16 | + time & an optional message. |
| 17 | + * To enable email notifications, the following preferences must be set in |
| 18 | + `~/.imagej/IJ_Prefs.txt`: |
15 | 19 | * .imcf.sender_email: sender's email address. |
16 | 20 | * .imcf.smtpserver: the SMTP server used for sending emails. |
17 | | - * If the sender email or SMTP server is not configured, method logs a message and exits. |
| 21 | + * If the sender email or SMTP server is not configured, method logs a |
| 22 | + message and exits. |
18 | 23 | * `imcflibs.imagej.misc.sanitize_image_title` to remove special chars and |
19 | 24 | various suffixes from an ImagePlus. |
20 | 25 | * `imcflibs.imagej.misc.subtract_images` to subtract an image from another. |
21 | 26 | * `imcflibs.imagej.misc.close_images` for closing selected image windows. |
22 | | - * `imcflibs.imagej.misc.get_threshold_value_from_method` to get the value that a selected AutoThreshold method would be using. |
23 | | - * `imcflibs.imagej.misc.write_orderddict_to_csv` to write data from an ordered dictionary to a CSV file. |
24 | | -* `imcflibs.imagej.labelimage.binary_to_label` for segmenting a binary image |
25 | | - to get a label image (2D/3D). |
26 | | -* `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. |
27 | | -* `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. |
| 27 | + * `imcflibs.imagej.misc.get_threshold_value_from_method` to get the value that |
| 28 | + a selected AutoThreshold method would be using. |
| 29 | + * `imcflibs.imagej.misc.write_orderddict_to_csv` to write data from an ordered |
| 30 | + dictionary to a CSV file. |
| 31 | +* `imcflibs.imagej.labelimage.binary_to_label` for segmenting a binary image to |
| 32 | + get a label image (2D/3D). |
| 33 | +* `imcflibs.imagej.misc.save_image_in_format` to save an ImagePlus image in a |
| 34 | + specified format, such as ImageJ-TIF or OME-TIFF etc., to a given directory. |
| 35 | +* `imcflibs.imagej.misc.run_imarisconvert` to convert a given file to Imaris |
| 36 | + format using the utility ImarisConvert. Method uses |
| 37 | + `imcflibs.imagej.misc.locate_latest_imaris` to find the path to the Imaris |
| 38 | + installation. |
28 | 39 |
|
29 | 40 | * New `imcflibs.imagej.objects3d` submodule, providing: |
30 | 41 | * `imcflibs.imagej.objects3d.population3d_to_imgplus` to turn |
@@ -64,8 +75,8 @@ As this is a major release, not all changes and functions are listed below. For |
64 | 75 | Dataset based on Interest Points" command. |
65 | 76 | * `imcflibs.imagej.bdv.duplicate_transformations` for duplicating / |
66 | 77 | propagating transformation parameters to other channels. |
67 | | - * `imcflibs.imagej.bdv.fuse_dataset` to call BigStitcher's "Fuse Multi-View Dataset" |
68 | | - command. |
| 78 | + * `imcflibs.imagej.bdv.fuse_dataset` to call BigStitcher's "Fuse Multi-View |
| 79 | + Dataset" command. |
69 | 80 | * New `imcflibs.imagej.trackmate` submodule to provide helper functions to interface with Trackmate: |
70 | 81 | * Multiple functions to set up Trackmate settings with different detectors, such as `cellpose`, `StarDist` or a `sparseLAP tracker`. |
71 | 82 | * `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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