5D Visualization and Annotation CATMAID Documentation

How to add new stack

1.-Log in catmaid/admin site
2.-Select Stacks Add (plus green sign)
3.-Fill in the text as shown in the figure
4.-Press save in the bottom right corner of the screen

Notes:
A.-Dimensions refers to the size of each volume in pixels (as in Fiji)

B.-Resolution refers to the pixel size in nm. It should be an integer number.

C.-Image base: crucial parameter to indicate where CATMAID can find the tiles. For example, if in the Matlab script (see section How to generate tiles) you saved the tiles into R:/data/12-08-28 then the image base is http://10.103.30.70/catmaid/data/12-08-28/stack1/, where 10.103.30.70 is the IP of the machine that was map to as drive R in this instance.

D.-Num zoom levels: is equal to maxScales – 1 (maxScales is a parameter in the Matlab script to generate tiles). //catmaid 和 matlab代码的对应关系！！！！！

E.-File extension, tile width and tile height has to match the parameters you used in the Matab script to generate the tiles.

F.-Tile source type: 5. This number indicates that we are using CATMAID for 5D images, instead of the original setup intended for 3D electron microscopy images.

G.-T refers to the total number of time points in the dataset. //catmaid 和 原始图片数据的对应关系！！！

H.-C refers to the total number of channels in the dataset. This number has to be in between square brackets. For example, [1] for datasets with a single channel.