Preparations and start

These are the necessary steps to start 3Dscript:

• Open a data set in Fiji.
  3Dscript works on single or multi-channel (composite) 8-bit or 16-bit images. Convert your image into this format if necessary
• Open the Brightness/Contrast tool (>Image>Adjust...>Brightness/Contrast) and the Channels tool (>Image>Color>Channels tool)
• Switch the display mode to "Color"
• Go through all channels and adjust minimum and maximum, i.e. black and white points, for each channel
• If required, adjust a channel's color in the Channels tool
• Now, start 3Dscript by clicking on >Plugins>3Dscript>Interactive Animation

In 2D, two values per channel, minimum and maximum displayed value, map signal strength to how bright a pixel is displayed. In 3D, each pixel has not only a brightness, but also a transparency. Transparency, like brightness, depends on the signal strength, i.e. pixels with a low signal are more transparent than pixels with a high signal. Like minimum and maximum displayed value in 2D define black and white point of a channel, corresponding values define opaque and fully transparent pixels in 3D. This means that in 3D, there are 4 parameters instead of two per channel, for brightness and transparency. In fact, 3Dscript supports non-linear interpolation between black and white point via gamma correction, for both brightness and transparency, so that there is a total of 6 parameters per channel.

3Dscript will choose default values for these parameters depending on the contrast setting in ImageJ. It is therefore highly recommended to carefully adjust the contrast before starting 3Dscript, to provide a good starting point.