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Updated README.md for mac
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heaslon committed Jun 18, 2015
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Expand Up @@ -11,7 +11,14 @@ Easy leaf area is free, open source, software that rapidly measures leaf area in
GETTING STARTED:
This program analyzes single jpeg or tiff images or batches of images for leaf area. Images must have a red scale of known area in the image in the same plane as the leaves for the program to use as a reference scale.

Download EasyLeafArea.zip and unzip the folder. To begin the program, Run ela.exe or ela.py (requires installation of Python® 2.7 ("Python" is a registered trademark of the Python Software Foundation”), Scipy, and Numpy, but you can modify the script to suit your needs). Open a single image by clicking the ‘Open an image’ button and navigating to and selecting the image. Adjust the ‘Scale area’ slider to the actual area of your red scale (It is set to 4.0 cm^2 when the program opens). Clicking ‘Auto settings’ will move the sliders on the right based on data in the image and measure leaf area. To calibrate ‘Auto settings’ see the AUTO SETTINGS CALIBRATION section below. After processing, the scale areas in the image should be red and the leaf areas green. If the automatic settings failed to identify all leaf area or scale area or identified background objects as scale or leaf area, you can manually adjust the settings sliders (See section on IMAGE ANALYSIS SETTINGS) on the right and click on the ‘Analyze with current settings’ button to rerun the analysis. Scale and leaf areas should be recolored based on your manual settings. If small groups of background pixels are misidentified as leaf area, they can be removed by selecting a ‘minimum leaf size’ greater than zero (WARNING: if there are many groups of misidentified background pixels, this can significantly add to processing time). Alternatively, if you only have one leaf per image, you can check ‘Only one leaf component’ and only the largest green component will be measured. To save the output ‘.tiff’ image and the pixel counts and leaf areas to a ‘.csv’ file, click on ‘Save analysis’. You can always click on “Save analysis’ first if you are confident that your settings will work. Only one image can be opened at a time, so you do not need to close one image before opening another.
Windows:
Download EasyLeafArea.zip and unzip the folder. https://github.com/heaslon/Easy-Leaf-Area/blob/master/EasyLeafArea.zip . To download the file click 'view the full file'. To begin the program, Run ela.exe or ela.py (requires installation of Python® 2.7 ("Python" is a registered trademark of the Python Software Foundation”), Scipy, and Numpy, but you can modify the script to suit your needs).

Mac:
Download mac executable 'ela' https://github.com/heaslon/Easy-Leaf-Area/blob/master/ela . To download the file click 'view the full file'. Double click the file to launch easy leaf area. If the file will not launch due to your security settings follow the instructions here: https://support.apple.com/kb/PH14369?locale=en_US . If the file opens as a text file, follow the instructions here: http://macosx.com/threads/change-a-plain-text-file-to-unix-executable-file.318118/ .

Windows and Mac:
Open a single image by clicking the ‘Open an image’ button and navigating to and selecting the image. Adjust the ‘Scale area’ slider to the actual area of your red scale (It is set to 4.0 cm^2 when the program opens). Clicking ‘Auto settings’ will move the sliders on the right based on data in the image and measure leaf area. To calibrate ‘Auto settings’ see the AUTO SETTINGS CALIBRATION section below. After processing, the scale areas in the image should be red and the leaf areas green. If the automatic settings failed to identify all leaf area or scale area or identified background objects as scale or leaf area, you can manually adjust the settings sliders (See section on IMAGE ANALYSIS SETTINGS) on the right and click on the ‘Analyze with current settings’ button to rerun the analysis. Scale and leaf areas should be recolored based on your manual settings. If small groups of background pixels are misidentified as leaf area, they can be removed by selecting a ‘minimum leaf size’ greater than zero (WARNING: if there are many groups of misidentified background pixels, this can significantly add to processing time). Alternatively, if you only have one leaf per image, you can check ‘Only one leaf component’ and only the largest green component will be measured. To save the output ‘.tiff’ image and the pixel counts and leaf areas to a ‘.csv’ file, click on ‘Save analysis’. You can always click on “Save analysis’ first if you are confident that your settings will work. Only one image can be opened at a time, so you do not need to close one image before opening another.

BATCH PROCESSING:
To batch analyze images for leaf area, first find settings that work for a few images you want to batch analyze or check use auto settings. When you are happy with the settings, select the source folder with images to analyze. Also select the write folder where highlighted output ‘.tiff’images and the ‘.csv’ output files will be saved.
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