===== FLEYE =====
FLEYE is a package of ImageJ macros developed to classify fly eyes attending to the distribution of their ommatidia using images of the eye surface as starting data. 


===== Authors =====
Cristina Rueda Sabater, Sergio Díez Hermano, Diego Sánchez Romero, María Dolores Ganfornina Álvarez and Jorge Valero Gómez-Lobo (jorge.valero@cnc.uc.pt)

===== Features =====
The FLEYE package includes three ImageJ macros that will allow the user to:
  * 1.- select in each image the regions of interest (ROI) for analysis, 
  * 2.- optimize parameters 
  * 3.- and analyze the images.

{{:plugin:analysis:fleye:fleye_menu.png|}}
===== Description =====

FLEYE package contains three macros created to:

1.- Sequentially design ROIs in the images to select the area to be analyzed (Fleye rois).

{{:plugin:analysis:fleye:roi_design.png|}}

2.- Optimize parameters: rolling ball radius and Find Maxima noise Tolerance (Fleye optimizer).

{{:plugin:analysis:fleye:optimization.png|}}

3.- Analyze ommatidia (Fleye analyzer) using the model published in "Diez-Hermano, Valero J, Rueda C, Ganfornina MD and Sanchez D. An automated image analysis method to measure regularity in biological patterns: a case study in a Drosophila neurodegenerative model. Molecular Neurodegeneration 2015, 10:9 (DOI 10.1186/s13024-015-0005-z)".

{{:plugin:analysis:fleye:table_results.png|}}

===== Installation =====
Unzip the {{:plugin:analysis:fleye:fleye2_2.zip|}} or individual macro files into the plugins folder of FIJI. 

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To solve the issue of malfunction due to FIJI updates we have also included the version of FIJI used when developing FLEYE plugin in FIJI_with_FLEYE.zip files (available for Win32  and Win64). 


===== Downloads =====

**Compressed packages:**

  * Compressed FLEYE package: {{:plugin:analysis:fleye:fleye2_2.zip|}}
  * FIJI version for Windows 32 bits with FLEYE: {{:plugin:analysis:fleye:fiji-win32_with_fleye.zip|}}
  * FIJI version for Windows 64 bits with FLEYE: {{:plugin:analysis:fleye:fiji-win64_withfleye.zip|}}

 
**Uncompressed macros:**

  * Fleye menu: {{:plugin:analysis:fleye:fleye_menu_v2.2.ijm|}}
  * Fleye rois: {{:plugin:analysis:fleye:fleye_roisv1.3.ijm|}}
  * Fleye optimizer: {{:plugin:analysis:fleye:fleye_optimizer_v4.3.ijm|}}
  * Fleye analyzer: {{:plugin:analysis:fleye:fleye_v10.5.ijm|}}

**Guides:**

  * Quick guide: {{:plugin:analysis:fleye:fleye_quick_guide.pdf|}}
  * User manual: {{:plugin:analysis:fleye:fleye_guide.pdf|}}


**Old versions:**
  * Fleye menu: {{:plugin:analysis:fleye:fleye_menu_v2.ijm|}}
  * Fleye rois: {{:plugin:analysis:fleye:fleye_roisv1.2.ijm|}}
  * Fleye optimizer: {{:plugin:analysis:fleye:fleye_optimizer_v4.2.ijm|}}
  * Fleye analyzer: {{:plugin:analysis:fleye:fleye_v10.4.ijm|}}

===== References/Citation =====
  * Diez-Hermano, Valero J, Rueda C, Ganfornina MD and Sanchez D. An automated image analysis method to measure regularity in biological patterns: a case study in a Drosophila neurodegenerative model. Molecular Neurodegeneration 2015, 10:9 (DOI 10.1186/s13024-015-0005-z)



===== License =====
GNU General Public License
FLEYE is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

FLEYE is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the [[http://www.gnu.org/copyleft/gpl.html|GNU General Public License]] for more details.

Copyright (C) 2014 Cristina Rueda Sabater, Sergio Díez Hermano, Diego Sánchez Romero, María Dolores Ganfornina Álvarez and Jorge Valero Gómez-Lobo (jorge.valero@cnc.uc.pt).

===== Changelog =====

== 17.06.2015 ==

New versions:

fleye2_2.zip

Fleye menu: fleye_menu_v2.2.ijm
Fleye rois: fleye_roisv1.3.ijm
Fleye optimizer: fleye_optimizer_v4.3.ijm
Fleye analyzer: fleye_v10.5.ijm

Change in Bioformats importer options (autoscale added) to solve some problems when opening images with FIJI running ImageJ version 1.49u.



== 16.03.2015 ==

fleye_optimizer_v4.3.ijm

fleye_v10.5.ijm

Spelling correction in parameters menu 


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===== Known Bugs =====