**Installation**
-----------------------------

**System requirements**
~~~~~~~~~~~~~~~~~~~~~~~~
VisuAlign uses files generated for and by QuickNII. VisuAlign
therefore has the same image requirements as QuickNII:

Standard web-compatible image formats are supported, 24-bit PNG and JPEG. Images can be loaded up to the resolution of 16 megapixels (e.g.
  4000x4000 or 5000x3000 pixels). However, just like QuickNII, VisuAlign does not benefit from image resolutions exceeding
  the resolution of the monitor in use. For a standard FullHD or WUXGA
  display (1920x1080 or 1920x1200 pixels) the useful image area is
  approximately 1500x1000 pixels, using a similar resolution ensures
  optimal image-loading performance and also eliminates excess storage
  size. As fulfilling these requirements usually requires preprocessing
  of the images (converting to PNG or JPEG and downscaling to
  screen-like size),
VisuAlign keeps track of original image dimensions as part of its series descriptor.

**Technical information**

VisuAlign is implemented in Java, with the graphical user interface built using JavaFX and FXML. While internally there are components and modules, like a slicer from QuickNII; the binary distributables are compiled with J-Link.


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

**Licence:** 

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


**Citation of VisuAlign:**

RRID on SciCrunch: (VisuAlign, RRID:SCR_017978)

* Puchades M, Yates SC, Csucs G, Carey H, Balkir A, Leergaard T, Bjaalie J.
    Software and pipelines for registration and analyses of rodent brain image data in reference atlas space. Frontiers of Neuroinformations. 2025. https://doi.org/10.3389/   fninf.2025.1629388 


* Gurdon B, Yates SC, Csucs G, Groeneboom NE, Hadad N, Telpoukhovskaia M, Ouellette A, Ouellette T, O’Connell KMS, Singh S, Murdy TJ, Merchant E, Bjerke I, Kleven H,      Schlegel U, Leergaard TB, Puchades MA, Bjaalie JG, and Kaczorowski CC.
   Detecting the effect of genetic diversity on brain composition in an Alzheimer’s disease mouse model. Nature Communications Biology, 2024; 7(605) https://doi.org/10.1038/s42003-024-06242-1


**Download**
~~~~~~~~~~~~~~~~~~
Link: https://www.nitrc.org/projects/visualign 

Unzip the VisuAlign folder at your desired location.


**Versions and release notes**


* Version 0.9 (2021-10-11) 

* Version 0.8 (2020-01-23) First stable version