update README

README.md

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-# Ronny_Bergmann_AirtrackMotorPlanning_TrackedEyePositions
+# Eye tracking data for: Bergmann, Sehara _et al._, 2022
+
+[DeepLabCut](http://www.mackenziemathislab.org/deeplabcut/)-aided pupil-position tracking data for the "AirtrackMotorPlanning" project (examines whether whiskers and pupil positions predict the animal's motor plans).
+
+### Contents
+
+- [File organization](#file-organization)
+- [Drawing eyelids](#drawing-eyelids)
+
+
+
+## File organization
+
+### File names
+
+The files are (mostly) organized as: `<ANIMAL>/<SESSION>/<DOMAIN>/<ANIMAL>_<SESSION>_<DOMAIN>_run<TRIAL>`, where:
+
+- `ANIMAL` representing the ID of the animal (in the pattern `MLAxxxxxx`).
+- `SESSION` being the name of the session (in the pattern `sessionYYYY-MM-DD-001`).
+- `DOMAIN` representing the domain of recording (see below).
+- `TRIAL` being the trial index during the session.
+
+### Domain names
+
+| Domain name  | Description                                                  |
+| ------------ | ------------------------------------------------------------ |
+| left         | CSV files containg the coordinates related to the left eye (in pixels). |
+| left-eyelid  | PNG files of average projection images of the left eye during each trial, and CSV files representing the manually-drawn upper and lower eyelids. |
+| right        | CSV files containg the coordinates related to the right eye (in pixels). |
+| right-eyelid | PNG files of average projection images of the right eye during each trial, and CSV files representing the manually-drawn upper and lower eyelids. |
+
+## Drawling eyelids
+
+Based on the average-projection images, the top and the bottom eyelids were drawn manually using the freehand selection tool of [ImageJ](https://imagej.nih.gov/ij/). The ROIs were then exported using the [SaveEyelidROI.ijm](SaveEyelidROI.ijm) macro.
+
+----
+
+Copyright (c) 2022, Ronny Bergmann, [Keisuke Sehara](https://orcid.org/0000-0003-4368-8143), Sina E. Dominiak, [Julien Colomb](https://orcid.org/0000-0002-3127-5520), [Jens Kremkow](https://orcid.org/0000-0001-7077-4528), [Matthew E. Larkum](https://orcid.org/0000-0001-9799-2656), [Robert N. S. Sachdev](https://orcid.org/0000-0002-6627-0199), [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/)
 
-DeepLabCut-aided pupil-position tracking data for the "AirtrackMotorPlanning" project (examines whether whiskers and pupil positions predict the animal's motor plans).

SaveEyelidROI.ijm

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+Dialog.create("Listing eyelid ROI...");
+Dialog.addChoice("which eyelid?", newArray("Top", "Bottom"));
+Dialog.show();
+
+channel = Dialog.getChoice();
+savename = replace(getTitle(), ".png", "-"+channel+".txt");
+savepath = getDirectory("image") + "/" + savename;
+fp = File.open(savepath);
+print(fp, "X,Y");
+Roi.getContainedPoints(xp, yp);
+for (i=0; i<xp.length; i++) {
+    print(fp, toString(xp[i]) + "," + toString(yp[i]));
+}
+showMessage("saved as: "+savename);