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Program to flatten retinal image stacks using 2 immunolabeled layers (such as choline acetyltransferase, CHaT)
or using a single layer (such as melanopsin), and up to 2 additionally labeled channels can be flattened based on this.
See our documentation.
Our new Fiji plugin for Windows! (Fiji is available here.)
Our Windows program (this is an older version).
If used you can cite our paper on the M5 cell, a color-opponent ipRGC:
http://www.cell.com/neuron/fulltext/S0896-6273(17)31083-8
Stabio ME, Sabbah S, Quattrochi LE, Ilardi MC, Fogerson PM, Leyrer ML, Kim MT, Kim I, Schiel M, Renna JM, Briggman KL, Berson DM. The M5 Cell: A Color-Opponent Intrinsically Photosensitive Retinal Ganglion Cell. Neuron. 2018 Jan 3;97(1):251.
Based on code from Sümbül, U. et al. A genetic and computational approach to structurally classify neuronal types. Nat. Commun. 5:3512 doi: 10.1038/ncomms4512, 2014
http://github.com/uygarsumbul/rgc
Other included code sources:
SliceBrowser, Copyright (c) 2010, Marian Uhercik
https://www.mathworks.com/matlabcentral/fileexchange/20604-3d-slice-viewer
gridfit, Copyright (c) 2016, John D'Errico
https://www.mathworks.com/matlabcentral/fileexchange/8998-surface-fitting-using-gridfit
tiffread, Copyright (c) 2016, Matthew Eicholtz
https://www.mathworks.com/matlabcentral/fileexchange/60037-tiffread
flexinterpn, Copyright (c) 2010, Jochen Weber
https://github.com/cjhammond/neuroelf
peakdet, Eli Billauer
http://www.billauer.co.il/peakdet.html