**Installation**
-----------------------------
**System requirements**
~~~~~~~~~~~~~~~~~~~~~~~~
Microsoft Windows: 64-bit operating system, Windows 7 or later

Apple macOS: OS X 10.9 (Mavericks) or later

3 gigabytes RAM

Display resolution minimum 1440 pixels wide and minimum 650 pixels high.

**Technical information**

QuickNII consists of two co-located executable components implemented in
two programming languages for historical reasons. The GUI component is
implemented in MXML+ActionScript (runs on Adobe Integrated Runtime,
which is bundled as "captive runtime", requiring no installation). A
slicer service running in the background is implemented in Java (and has
a bundled JRE requiring no installation). The two components communicate
via standard output and local TCP connections (using the loopback
interface).

**Conditions of use**
~~~~~~~~~~~~~~~~~~~~~~

**Licence:** 

Creative Commons Attribution-NonCommercial-ShareAlike 4.0
International for the main component. Source code: MIT License.


**Citation of the tool:**

-RRID on SciCrunch: (QuickNII, RRID:SCR_016854)

-Puchades MA, Csucs G, Ledergerber D, Leergaard TB, Bjaalie JG (2019)
  Spatial registration of serial microscopic brain images to
  three-dimensional reference atlases with the QuickNII tool. PLOS ONE
  14(5): e0216796. https://doi.org/10.1371/journal.pone.0216796

**Download**
~~~~~~~~~~~~~
Download of the software is from Nitrc.org
Link: https://www.nitrc.org/projects/quicknii/ 

Unzipp the QuickNII folder at your desired location.


**Versions and release notes**

* Version 2.2 (2019-05-28) This release includes several reference atlases.
Linux support was added in July 2020. 

* Version 2.2preview (2019-04-02) Series descriptor builder recognizes multiple numbering variants in filenames (numbers at fixed character position from either end of names, and sequence indicator \_s prefixanywhere) 
Coordinate transformation to/from Allen CCFv3 added to Mouse package.

* Version 2.1 (2018-12-05) First stable version