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Trajectories analysis_​L-D transition assay zebrafish

L/D zebrafish transition assay analysis

This workflow analyses the trajectories of zebrafish larvae in 24 well-plate. Is adapted for the analysis of one plate with different videos representing the light/dark cycles.


Set up threshold for ligth/dark cycles usingfile name KNIME workflow for the analysis of larvae trajectories in 24 well-platesRequired Knime extensions: external tool support, image processing, Interactive R statistics integrationFfmpeg software: ffmpeg software: https://ffmpeg.org/download.html Please if you use the workflow give credit to E.TeixidóPublication coming soon Time filter (optional)Default (all selected from 1 to 16) 3. Trajectories analysis 2. Create plate layout Insert plate layout 1. Video (.avi) to frames (.tif) Node 489Node 531Node 577Node 578Node 580Creates directory(may fail in caseof spaces in pathand file names)Creates path to .bat fileWrite temporary .bat fileWait until .bat fileis createdRun temporary.bat file for ffmpegIncrease sizeCreate time range depending on frame rateNode 1696Node 1702Node 1710Node 1711Node 1732Split \ImageNode 1734Check layoutMark wellsLabels to WellNode 1742Node 1743List folderwith video framesNode 1773ExecuteNode 1775Node 1776OptionalopcionalNode 1782Default 50pxFilter one cycleNode 1798Add .table extensionNode 1811Node 1812Node 1814OptionalList folder with layoutNode 1865Set a different thresholdfrom light to dark cyclesNode 1867HiLite selection (optional)Node 1869Node 1870List folders with video files (.avi)List folder withligth/dark cycle of one plateWrites a file.table with layoutAutomatic path creationNode 1879Image folder selectionNode 1881Node 1883Node 1884Node 1887Node 1888Node 1889Node 1890Table Row to Variable(deprecated) String Manipulation Labeling toPNG Images Split CollectionColumn RowID Directory creation Path to ffmpeg CSV Writer(deprecated) Wait... External Tool Resize Table Creator R View (Table) Row Splitter Excel Writer Image To Table Total distance Distance Cross Joiner Cell Splitter String to Path(Variable) InteractiveSegmentation View InteractiveAnnotator Table Creator Joiner (deprecated) Joiner (deprecated) List Files/Folders Path to String(Variable) Loop End(deprecated) Chunk Loop Start Table Rowto Variable Cycle analysis Excel Writer Row Filter Row Filter StructuringElement Creator Row Filter RowID String Manipulation Table Rowto Variable Path to String ReferenceRow Filter Row Filter List Files/Folders Row Filter Rule Engine Table Rowto Variable HiLite Row Splitter Table Row ToVariable Loop Start Loop End List Files/Folders List Files/Folders Table Writer String to Path(Variable) Read first frame List Files/Folders Path to String Missing ValueColumn Filter Cross Joiner Variable toTable Row Cross Joiner Num file Load layout Set up threshold for ligth/dark cycles usingfile name KNIME workflow for the analysis of larvae trajectories in 24 well-platesRequired Knime extensions: external tool support, image processing, Interactive R statistics integrationFfmpeg software: ffmpeg software: https://ffmpeg.org/download.html Please if you use the workflow give credit to E.TeixidóPublication coming soon Time filter (optional)Default (all selected from 1 to 16) 3. Trajectories analysis 2. Create plate layout Insert plate layout 1. Video (.avi) to frames (.tif) Node 489Node 531Node 577Node 578Node 580Creates directory(may fail in caseof spaces in pathand file names)Creates path to .bat fileWrite temporary .bat fileWait until .bat fileis createdRun temporary.bat file for ffmpegIncrease sizeCreate time range depending on frame rateNode 1696Node 1702Node 1710Node 1711Node 1732Split \ImageNode 1734Check layoutMark wellsLabels to WellNode 1742Node 1743List folderwith video framesNode 1773ExecuteNode 1775Node 1776OptionalopcionalNode 1782Default 50pxFilter one cycleNode 1798Add .table extensionNode 1811Node 1812Node 1814OptionalList folder with layoutNode 1865Set a different thresholdfrom light to dark cyclesNode 1867HiLite selection (optional)Node 1869Node 1870List folders with video files (.avi)List folder withligth/dark cycle of one plateWrites a file.table with layoutAutomatic path creationNode 1879Image folder selectionNode 1881Node 1883Node 1884Node 1887Node 1888Node 1889Node 1890Table Row to Variable(deprecated) String Manipulation Labeling toPNG Images Split CollectionColumn RowID Directory creation Path to ffmpeg CSV Writer(deprecated) Wait... External Tool Resize Table Creator R View (Table) Row Splitter Excel Writer Image To Table Total distance Distance Cross Joiner Cell Splitter String to Path(Variable) InteractiveSegmentation View InteractiveAnnotator Table Creator Joiner (deprecated) Joiner (deprecated) List Files/Folders Path to String(Variable) Loop End(deprecated) Chunk Loop Start Table Rowto Variable Cycle analysis Excel Writer Row Filter Row Filter StructuringElement Creator Row Filter RowID String Manipulation Table Rowto Variable Path to String ReferenceRow Filter Row Filter List Files/Folders Row Filter Rule Engine Table Rowto Variable HiLite Row Splitter Table Row ToVariable Loop Start Loop End List Files/Folders List Files/Folders Table Writer String to Path(Variable) Read first frame List Files/Folders Path to String Missing ValueColumn Filter Cross Joiner Variable toTable Row Cross Joiner Num file Load layout

Nodes

Extensions

Links

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
Created by: Elisabet
Created at: 2023-03-08
On NodePit since: 2023-04-05
Last update: 2024-04-27
Created with KNIME version: v4.7.1
Tags: zebrafishffmpegimage analysismoving averageR ggplottrajectories

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