Differences
This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision | ||
setup:data_configuration [2019/07/11 13:10] – pseudomoaner | setup:data_configuration [2020/06/03 19:41] (current) – pseudomoaner | ||
---|---|---|---|
Line 1: | Line 1: | ||
- | ===== Data setup and configuration ===== | + | ====== Data setup and configuration |
- | The FAST pipeline analyses each imaging dataset within a unique directory, referred to throughout this manual as the ' | + | ===== Supported |
- | For large experiments consisting | + | FAST uses [[https:// |
- | \\ | + | * Tagged image files (.tif/ |
+ | * Zeiss microscopy images (.czi) | ||
+ | * Zeiss laser-scanning microscopy images (.lsm) | ||
+ | * Nikon NIS-elements images (.nd2) | ||
+ | * Leica image file format images (.lif) | ||
- | < | + | among many others. For a full list, see [[https:// |
- | | RRR | | | | | | | | | | | |RRR{background-color:# | + | |
- | | |!| | | | | | | | | | | | | | + | |
- | | |)|-|-| EE1 | | | | | | | |EE1{background-color:# | + | |
- | | |!| | | |!| | | | | | | | | | + | |
- | | |!| | | |)|-| RE1 | | | | |RE1{background-color:# | + | |
- | | |!| | | |!| | |!| | | | | | | + | |
- | | |!| | | |!| | |`|-|-| IM1 |IM1{background-color:# | + | |
- | | |!| | | |!| | | | | | | | | | + | |
- | | |!| | | |)|-| RE2 | | | | |RE2{background-color:# | + | |
- | | |!| | | |!| | | | | | | | | | + | |
- | | |!| | | |`|-| RE3 | | | | |RE3{background-color:# | + | |
- | | |!| | | | | | | | | | | | | | + | |
- | | |)|-|-| EE2 | | | | | | | |EE2{background-color:# | + | |
- | | |!| | | | | | | | | | | | | | + | |
- | | |`|-|-| EE3 | | | | | | | |EE3{background-color:# | + | |
- | </ | + | |
- | \\ | + | <note tip> |
+ | In some cases, it may be useful to pre-process image data using [[https:// | ||
+ | </ | ||
+ | |||
+ | ===== File structure ===== | ||
+ | |||
+ | The FAST pipeline analyses each imaging dataset within a unique directory, referred to throughout this manual as the ' | ||
+ | |||
+ | For large experiments consisting of many individual image series, each separate image file should be placed in a separate directory. For example, we may have collected data under several different experimental conditions, with several replicates of each condition. In this case we might set up our directory structure as shown: | ||
+ | |||
+ | {{ : | ||
< | < | ||
Line 33: | Line 31: | ||
Once a single image series has been analysed using the FAST GUI, other datasets within the experiment can be analysed using the same parameters with FAST's [[usage: | Once a single image series has been analysed using the FAST GUI, other datasets within the experiment can be analysed using the same parameters with FAST's [[usage: | ||
- | ==== Supported image formats ==== | ||
- | FAST uses [[bio-formats|https:// | ||
- | |||
- | * Tagged image files (.tif/ | ||
- | * Zeiss microscopy images (.czi) | ||
- | * Zeiss laser-scanning microscopy images (.lsm) | ||
- | * Nikon NIS-elements images (.nd2) | ||
- | * Leica image file format images (.lif) | ||
- | |||
- | among many others. For a full list, see [[https:// |