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Patrick Scheibe committed Feb 4, 2015
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Expand Up @@ -5,20 +5,23 @@ Mathematica Import for HEYEX Raw Data

This is a *Mathematica* package to access HEYEX Raw files which can e.g. created from Optical Coherence Tomography scans of [*Heidelberg Spectralis* products](http://www.heidelbergengineering.com/us/products/spectralis-models/).

The package incorporates its functionality directly into the `Import`-framework of *Mathematica*. Therefore, Heyex Raw files can be loaded by calling `Import` as specified in the [Usage section](#Usage).
The package incorporates its functionality directly into the [`Import`-framework of *Mathematica*](http://reference.wolfram.com/language/ref/Import.html). Therefore, Heyex Raw files can be loaded by calling `Import` as specified in the [Usage section](#Usage).

Various information of the Heyex files can be accessed:

- The file header which contains meta data like patient ID's, scan sizes, etc.
- The scanned volume data as a numerical array
- The scanned volume as `Image3D`
- Slices or the whole volume as a list of `Image`s
- The *scanning laser ophthalmoscopy* (SLO) image
- The segmentation data for different retina layers (ILM, RPE) when provided in the HEYEX Raw file
- The scanned volume as [`Image3D`](http://reference.wolfram.com/language/ref/Image3D.html)
- Slices or the whole volume as a list of [`Images`](http://reference.wolfram.com/language/ref/Image.html)
- The [*scanning laser ophthalmoscopy* (SLO)](http://en.wikipedia.org/wiki/Scanning_laser_ophthalmoscopy) image
- The segmentation data for different retina layers ([ILM][ilm], [RPE](rpe)) when provided in the HEYEX Raw file

[ilm]: http://en.wikipedia.org/wiki/Inner_limiting_membrane
[rpe]: http://en.wikipedia.org/wiki/Retinal_pigment_epithelium

##![Install Icon](http://i.imgur.com/ayLRwo3.png) Installation

Download or clone the repository and copy the *inner* `HeyexImport` directoy with all content:
[Download](https://github.com/halirutan/HeyexImport/archive/master.zip) or clone the repository and copy the *inner* `HeyexImport` directoy with all content:

HeyexImport
├── HeyexImport.m
Expand All @@ -33,8 +36,7 @@ After that, you should be able to load the package with

<<HeyexImport`

Note that the package does only provide one function `HeyexEyePosition`. All the import functionality is directly incorporated into the
normal `Import` built-in function.
Note that the package does only provide one function `HeyexEyePosition`. All the import functionality is directly incorporated into the normal `Import` built-in function.

##![Usage Icon](http://i.imgur.com/iZbiTUl.png) Usage

Expand Down Expand Up @@ -107,3 +109,9 @@ To specify several just use a list:
Import[file, {"Heyex", "FileHeader", {"SizeX", "NumBScans", "SizeXSlo"}}]

##![Contact Icon](http://i.imgur.com/f15dshA.png) Contact

If you find bugs or experience unusual behavior you might want to [open an issue](https://github.com/halirutan/HeyexImport/issues) and describe your problems. If you like to contact me for other reasons, please write me an email. For my mail-address please evaluate the following *Mathematica* code

Uncompress["1:eJxTTMoPCpZmYGAoKE7OSM1MSnUoKcrVK83L1M1JzSyoykzXS0kFAM0/DBs="]

If you have more *Mathematica* question, you are probably interested in some of [my answers on Mathematica.stackexchange.com](http://mathematica.stackexchange.com/users/187/halirutan?tab=answers&sort=votes).

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