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--- setup:data_configuration [2019/07/11 13:11] – [Supported image formats] 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 'root' directory. Initially, this directory should be set up to contain a single image file, which can contain multiple channels and timepoints. Three-dimensional images consisting of multiple z-positions are not currently supported.
+===== 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:
+FAST uses [[https://www.openmicroscopy.org/bio-formats/|bio-formats]] to open a range of different image formats. These include:
-\\
+  * Tagged image files (.tif/.tiff)
+  * Zeiss microscopy images (.czi)
+  * Zeiss laser-scanning microscopy images (.lsm)
+  * Nikon NIS-elements images (.nd2)
+  * Leica image file format images (.lif)
-<diagram>
+among many others. For a full list, see [[https://docs.openmicroscopy.org/bio-formats/6.1.1/supported-formats.html|this page]].
-| RRR | | | | | | | | | | | |RRR{background-color:#ccffff}=Root
-| |!| | | | | | | | | | | | |
-| |)|-|-| EE1 | | | | | | | |EE1{background-color:#ccffcc}=Experiment 1
-| |!| | | |!| | | | | | | | |
-| |!| | | |)|-| RE1 | | | | |RE1{background-color:#ffffcc}=Replicate 1
-| |!| | | |!| | |!| | | | | |
-| |!| | | |!| | |`|-|-| IM1 |IM1{background-color:#ffcccc}=Image.tif
-| |!| | | |!| | | | | | | | |
-| |!| | | |)|-| RE2 | | | | |RE2{background-color:#ffffcc}=Replicate 2
-| |!| | | |!| | | | | | | | |
-| |!| | | |`|-| RE3 | | | | |RE3{background-color:#ffffcc}=Replicate 3
-| |!| | | | | | | | | | | | |
-| |)|-|-| EE2 | | | | | | | |EE2{background-color:#ccffcc}=Experiment 2
-| |!| | | | | | | | | | | | |
-| |`|-|-| EE3 | | | | | | | |EE3{background-color:#ccffcc}=Experiment 3
-</diagram>
-\\
+<note tip>
+In some cases, it may be useful to pre-process image data using [[https://fiji.sc/|FIJI]]/[[https://imagej.nih.gov/ij/|ImageJ]] prior to tracking with FAST. In these cases, it is recommended that hyperstacks be saved as OME-TIFFs to maximise compatibility with bio-formats.
+</note>
+===== File structure =====
+The FAST pipeline analyses each imaging dataset within a unique directory, referred to throughout this manual as the 'root' directory. Initially, this directory should be set up to contain a single image file, which can contain multiple channels and timepoints. Three-dimensional images consisting of multiple z-positions are not currently supported.
+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:
+{{ :setup:setupfiles.png?nolink&300 |}}
 <note>
@@ 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:batch processing]] system.
-==== Supported image formats ====
-FAST uses [[https://www.openmicroscopy.org/bio-formats/|bio-formats]] to open a range of different image formats. These include:
-  * Tagged image files (.tif/.tiff)
-  * 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://docs.openmicroscopy.org/bio-formats/6.1.1/supported-formats.html|this page]].