Commit f71d1f92 authored by Guillaume Blin's avatar Guillaume Blin

Updated notes on image quality

parent 04794719
......@@ -55,11 +55,11 @@ Image quality is critical to get right for image quantification purpose. It is e
Below is a list of image properties that are strongly recommended for Nessys segmentation :
* **Bit depth :** 16 bits. This is a very important parameter, almost obligatory. This defines the number of gray values that each voxel can code. The difference for the eye may be null but it makes a huge difference to the computer.
* **Bit depth :** The bit depth defines the range of gray values that each pixel can display. This may be important for some applications but in our hands, Nessys works equally fine on 12 bits or 8 bits images. If file size is not an issue, we would still recommend using 12bits acquisition or higher.
* **XY resolution :** 0,1 µm – 0,6 µm. The denser and elongated the cells are, the higher the XY resolution should be. Both accuracy and segmentation time will increase with resolution.
* **Z-step size :** 0,1 µm – 2 um. Nessys first segments each z-slice independently and then links 2D segmented shapes into 3D objects. The smaller the z-step the more robust the segmentation will be. Larger z-step sizes are acceptable when cells are not flat (3D culture, embryos), however, for 2D culture it is recommended not to go above 0,5 µm.
* **Z-step size :** 0,1 µm – 1.5 µm. Nessys first segments each z-slice independently and then links 2D segmented shapes into 3D objects. The smaller the z-step the more robust the segmentation will be. Larger z-step sizes are acceptable when cells are not flat (3D culture, embryos), however, for 2D culture it is recommended not to go above 0,5 µm.
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