RetFM-J

RetFM-J

Authors: Mark Christopher, Adam Hedberg-Buenz, Todd E. Scheetz, Michael D. Abramoff, and Michael G. Anderson

History: 2015/08/28: Initial release
2015/10/06: Outputs a single spreadsheet

Source: Download RetFM_J.java

Installation: Drag and drop RetFM_J.jar to the "ImageJ" window or download and install using the Plugins>Install command, and an "RetFM J" command will appear in the Plugins menu.

Description: RetFM-J counts, segments, and computes quantitative features of cell nuclei in the inner retina from images of hematoxylin and eosin (H&E)-stained retinal whole-mounts.
Local contrast enhancement is performed using the CLAHE plugin. Fiji includes this functionality by default. ImageJ users, however, should install this plugin from the link above. Since publication of the manuscript referenced above, the RetFM-J plugin has been amended to output all data (i.e. the number of nuclei counted, feature information for each nucleus, and area measurements for all analyzed images) in a single spreadsheet rather than in three separate files as described in the manuscript.
For guidance on the use of RetFM-J, detailed instruction may be found in the manuscript referenced below.
Test images: Included are a high density test image and a low density test image, captured at a total magnification of 200X (1360 x 1024 px) from whole-mounted retinas stained with H&E for preliminary test runs of RetFM-J. The image exhibiting a high density of nuclei is from a mouse with no overt disease (C57BL/6J). The image with a low density of nuclei is from the diseased retina of a mouse with glaucoma (DBA/2J).

Reference: Hedberg-Buenz et. al. RetFM-J, an ImageJ-based module for automated counting and quantifying features of nuclei in retinal whole-mounts. Exp Eye Res (2015). [PMID: 26283021].

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Authors:	Mark Christopher, Adam Hedberg-Buenz, Todd E. Scheetz, Michael D. Abramoff, and Michael G. Anderson
History:	2015/08/28: Initial release 2015/10/06: Outputs a single spreadsheet
Source:	Download RetFM_J.java
Installation:	Drag and drop RetFM_J.jar to the "ImageJ" window or download and install using the Plugins>Install command, and an "RetFM J" command will appear in the Plugins menu.
Description:	RetFM-J counts, segments, and computes quantitative features of cell nuclei in the inner retina from images of hematoxylin and eosin (H&E)-stained retinal whole-mounts. Local contrast enhancement is performed using the CLAHE plugin. Fiji includes this functionality by default. ImageJ users, however, should install this plugin from the link above. Since publication of the manuscript referenced above, the RetFM-J plugin has been amended to output all data (i.e. the number of nuclei counted, feature information for each nucleus, and area measurements for all analyzed images) in a single spreadsheet rather than in three separate files as described in the manuscript. For guidance on the use of RetFM-J, detailed instruction may be found in the manuscript referenced below. Test images: Included are a high density test image and a low density test image, captured at a total magnification of 200X (1360 x 1024 px) from whole-mounted retinas stained with H&E for preliminary test runs of RetFM-J. The image exhibiting a high density of nuclei is from a mouse with no overt disease (C57BL/6J). The image with a low density of nuclei is from the diseased retina of a mouse with glaucoma (DBA/2J).
Reference:	Hedberg-Buenz et. al. RetFM-J, an ImageJ-based module for automated counting and quantifying features of nuclei in retinal whole-mounts. Exp Eye Res (2015). [PMID: 26283021].