Introduction
This is a packaged version of FijiWings for Mac and Windows, a set of macros designed to perform semi-automated morphophometric analysis of a wing photomicrograph. FijiWings uses plug-ins installed in the Fiji version of ImageJ to rapidly and accurately measure wing area, reliably detect trichome positions and calculate trichome density of a wing region selected by the user.
Licensing
This plugin is free software, licensed under the GNU GPL v3 so please do contribute any patches or suggestions that you think would be useful. Please email me at dobensl@umkc.edu with any feedback.
Installation
For the Mac:
(1) FijiWings2.4 is distributed as packaged version of Fiji - to install it, download the file
fiji-macosx-20201207055513.zip
from the Fijiwings for Mac folder found at https://sourceforge.net/projects/fijiwings/files/?source=navbar, unzip and drag/place in Applications folder. The downloaded package is named Fiji . This name must be changed to Fijiwings2.4 .
(2) Next, download the file data.arff from the same Fijiwings for Mac folder found at https://sourceforge.net/projects/fijiwings/files/?source=navbar.
(3) Open up the packaged Fijiwings2.4 Application by control-clicking "Show package contents"
(4) Once package contents are open, drag the data.arff file into Fijiwings2.4.app>Plugins>ActionBar folder. All this is a hassle, but the Segmentation function will not work unless it finds the data.arff file in that location.
(5) Launching Fijiwings2.4 for the first time requires you to go to Systems Preferences/Security & Privacy and click the radio button on Allow Apps downloaded from SourceForge selection.
UPDATE 12-9-20
Fijiwings2.4 for Mac now packages Java and its installation is a bit simpler. Hooray!
For Windows:
FijiWings2.2 is the current Windows versions and is distributed as packaged version of Fiji - to install it, download the file Fiji.app.zip from the Fijiwings for Windows folder at https://sourceforge.net/projects/fijiwings/files/?source=navbar, unzip and drag/place in C:\\Programs folder (another copy of Fiji can NOT co-exist in the folder).
Launching Fijiwings2.2 for the first time results in a warning asking you to Extract files or Run the program. Do not click on Extract files as this overwrites the macro attached to the program and erases plug-ins ActionBar and ROI Heat Map . Rather, check the box do not show this warning again and click Run.
Feedback
Please report any bugs that you find with Fiji's "Help > Report a Bug" menu option. For other feedback please email dobensl at umkc.edu. There are other ways of giving feedback on Fiji (e.g. the mailing lists, IRC, etc.) listed at Help:Contents.
Citing Fijiwings
If you would like to reference FijiWings in a publication, you can cite:
FijiWings: an open source toolkit for semi-automated morphometric analysis of insect wings, Alexander C. Dobens and Leonard L. Dobens, G3 (Bethesda). 2013 Aug 7;3(8):1443-9. doi: 10.1534/g3.113.006676.
Tutorials
http://www.youtube.com/watch?v=rz_rBDhrQ5Y
Technical Documentation
see http://sourceforge.net/projects/fijiwings
Authors
These macros were written by Alexander Dobens with feedback and direction from Anna Shipman and Leonard Dobens:
Many thanks to all of those authors for releasing their code under the GPL.
Known instabilities
Weka segmentation instabilities that plagued Fijiwings 2.1 appear to be fixed in this version.
Glitches such as failure to restrict the detection of trichomes to specific areas or intervein segments are often rectified by simply repeating the task. At times, especially after many measurements, we find it necessary to quit the application and start again.
Updates:
10-24-19 Minor changes to Weka Segmentation to make it more stable. First, by renaming a the Weka window, update names included on the initial window do not cause a problem with subsequent steps (Thanks to Pradeep Rajasekhar on ImageJ forum). Second, by changing "run("Fill Holesî);î to "run(ñClose-î);î the handling of the segmented image is made simpler for a wider array of images (thanks, Annick Sawala)
2-25-19 Updated to latest version of Fiji. Packaged as Fijiwings2.3.tar.tar.gz and uploaded.
9-3-18 Fijiwings 2.3 (packaged for Fiji 1.52e, build bad6864e55) for Mac. Following steps above, will work with this current build of Fiji on MacBook Pro running High Sierra 10.13.6.
CHANGES: Segmentation 4GB is now removed - the delays in launching Weka segmentation written into the Macro code has increased stability enough to say goodbye to this. So now it is simply "segmentation". Also, the "intervein trichome density" places classified image at the front for selection of intervein directly, without having to first bring the window to the fore. Subtle thing, but increases ease of use.
10-3-17 Installed on MacBook Pro running Sierra following instructions above with no difficulties.
4-11-17 Fijiwings2.2 for the Mac has been updated for the latest version of Fiji and is in the Fijiwings for Mac file (click on the file package fiji-macosx-20170410052924.tar.tar.bz2 , allow download, double-click to open and follow the instructions for installation detailed below). This version works on macOS Sierra.
12-28-15 The latest respective versions of Fijiwings have been uploaded. (1) Fijiwings2.2 for Windows is in the Fijiwings for Windows file (click on Fiji.app.zip ) and (2) Fijiwings2.2 for the Mac is in the Fijiwings for Mac file (click on Fijiwings2.2.zip ). The instructions for installation of each are detailed below. (Small bug that affects Fijiwings for Mac fixed on 1/12/16).
