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 18:57] – 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 image formats |
- | + | ||
- | 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: | + | |
- | + | ||
- | \\ | + | |
- | + | ||
- | < | + | |
- | | 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:# | + | |
- | </ | + | |
- | + | ||
- | \\ | + | |
- | + | ||
- | < | + | |
- | Each frame in the input dataset should consist of a single, contiguous set of pixels; FAST does not currently support multi-field tiles or multi-position imaging. For instructions on how to process these types of dataset, please refer to the [[extra: | + | |
- | </ | + | |
- | + | ||
- | 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 [[https:// | FAST uses [[https:// | ||
Line 45: | Line 13: | ||
among many others. For a full list, see [[https:// | among many others. For a full list, see [[https:// | ||
- | < | + | < |
In some cases, it may be useful to pre-process image data using [[https:// | 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: | ||
+ | |||
+ | {{ : | ||
+ | |||
+ | < | ||
+ | Each frame in the input dataset should consist of a single, contiguous set of pixels; FAST does not currently support multi-field tiles or multi-position imaging. For instructions on how to process these types of dataset, please refer to the [[extra: | ||
+ | </ | ||
+ | |||
+ | 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: | ||
+ | |||
+ |