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Spontaneous tail coilings-measurement

Spontaneous tail coiling detection in zebrafish
Conversion of avi-video to tif-frames for subsequent image analysisRequires that the program ffmpeg is installed! Initially (only once) you have to specify the location of the ffmpeg.exe (inside the metanode). Configure path to ffmpeg Modify frame rate (2nd part ffmpegcommand) if necessary The Table creator node contains the pixel value used tobin the position of the eggs and identify the same egg ineach video frame. From the centroid of the label themetanode searches labels in the other frames withsimilar position taken into account a difference of pixelsdetermined by the Table creator node. Modify the valueaccording to video resolution or movement of the eggs. Extract spontaneous tail coilings of zebrafish embryos from AVI videos Installation of ffmpeg program required. Required knime extensions: math formula, quickforms, community image analysis nodes, external tool nodeRequired R-packages: quantmod1. Initially communication with the ffmpeg program has to be set up (see green workflow area, set path in metanode before the external tool node, youtube video: https://www.youtube.com/watch?v=K-MOCliM7bY).2.The video to analyse should be inserted in the KNIME workspace, use the Explorer browse to select the folder containing the video. Alternatively, you can remove this node and leave a List node (without variable). 3. The workflow creates a folder with the same name as the video file analysed that contains the stack of images generated. After the analysis they should be removed to save disk space!4. In the wrapped metanode "Frequency analysis" the frame rate can be configure and should be the same for the ffmpeg program (metanode in the green area).5. Browse to select the folder containing the videos to analyse using the Explorer Browser node. 6. Adjust the threshold if necessary.7. Execute the "Loop end" node.Note: For manual analysis of tail contractions use the image viewer node and "manual check of frequency" metanode. The interactive Segmentation view allows to inspect if labels were correctly identify for each embryo.Tutorial on how to use the workflow coming soon...Please knowledge the workflow creation to: Dr. Stefan Scholz (Helmholtz Center for Environmental Research, UFZ, Leipzig).Dr. Elisabet Teixidó (University of Barcelona, Barcelona).Associated publications (submitted):Ogungbemi A., Massei R., Teixido E., Scholz S., Küster E. Optimization of the spontaneous tail coiling test for fast assessment of neurotoxic effects in the zebrafish embryo using an automated workflow in KNIME®. Neurotoxicology and teratology. Teixidó E., Klüver N., Ogungbemi A., Küster E., Scholz S. Evaluation of neurotoxic effects in zebrafish embryos by automatic measurement of early motor behaviours. Neuromethods. Teixidó, Elisabet, Klüver, Nils, Ogungbemi, Afolarin, Küster, Eberhard, & Scholz, Stefan. (2020). KNIME workflows for the evaluation of neurotoxic effects in zebrafish embryos by automatic measurement of early motor behaviours [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3835947 Threshold can be modified in configuration of componentnode. Negative values increase white pixels values andpositive values increase black pixel values Consult R documentation for definition of variables:smoothing factor (spar): https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/smooth.splineThreshold and noise cut: https://www.rdocumentation.org/packages/dpcR/versions/0.5/topics/test_peaks OPTIONAL: workflow to combine all results from different video files Run temporary.bat file for ffmpegWrite temporary .bat fileNode 23Wait until execution of .bat file is completedWait until .bat fileis createdList all video fileson folderNode 114Be sure to fill the eggs!Node 121Node 134Node 414Output takes the same name for the xls fileNode 452Node 453Node 454Node 455Node 456Node 461Node 463Node 465Node 466Node 467Node 471Node 472Node 473OptionalNode 475Node 478Node 489Node 493Node 504Node 506Node 507Node 508Extract name fileNode 510Node 512Node 513Node 514Select directorycontaining all excel filesNode 516Node 519Node 521Node 522DEFINE NAME .xlsJoin the File number to the column containing Name of the filesNode 526Pixel differenc binner positionNode 528Node 531Node 533Node 553Execute to analyseall videos in folderNode 556Layout to relateName of excel files to chemical concentration or treatmentNode 564Node 565optional for testingNode 577Node 578Node 579Node 580Node 1613Browse to select folder containingvideo filesCreates directory(may fail in caseof spaces in pathand file names)Creates path to .bat file External Tool CSV Writer(deprecated) List Files(deprecated) Wait... Wait... List Files(deprecated) Image Reader(Table) Global Thresholder ImageJ Macro Image SegmentFeatures XLS Sheet Appender(deprecated) XLS Writer(deprecated) Lag Column Image Calculator Global Thresholder Segment Cropper Joiner Joiner InteractiveSegmentation View Position binner Image Viewer Manual checkof frequency Sorter String Manipulation String To Number(deprecated) RowID Row Filter Median Filter Variable to TableRow (deprecated) Table Row to Variable(deprecated) Even or oddFrames filter Table Row to Variable(deprecated) Extract Variables(Data) Variable to TableRow (deprecated) Joiner Java Snippet(simple) RowID RowID XLS Reader(deprecated) XLS Reader(deprecated) List Files(deprecated) Table Row To VariableLoop Start (deprecated) Joiner Loop End Math Formula XLS Writer(deprecated) Joiner GroupBy Table Creator XLS Sheet Appender(deprecated) String Manipulation Image even orodd number Frequency analysis Mean frequency Loop End Table Row To VariableLoop Start (deprecated) Excel Reader (XLS)(deprecated) Joiner Check for error Row Filter Labeling toPNG Images Split CollectionColumn Joiner RowID Missing Value Explorer Browser Threshold Directory creation Path to ffmpeg Split labels Conversion of avi-video to tif-frames for subsequent image analysisRequires that the program ffmpeg is installed! Initially (only once) you have to specify the location of the ffmpeg.exe (inside the metanode). Configure path to ffmpeg Modify frame rate (2nd part ffmpegcommand) if necessary The Table creator node contains the pixel value used tobin the position of the eggs and identify the same egg ineach video frame. From the centroid of the label themetanode searches labels in the other frames withsimilar position taken into account a difference of pixelsdetermined by the Table creator node. Modify the valueaccording to video resolution or movement of the eggs. Extract spontaneous tail coilings of zebrafish embryos from AVI videos Installation of ffmpeg program required. Required knime extensions: math formula, quickforms, community image analysis nodes, external tool nodeRequired R-packages: quantmod1. Initially communication with the ffmpeg program has to be set up (see green workflow area, set path in metanode before the external tool node, youtube video: https://www.youtube.com/watch?v=K-MOCliM7bY).2.The video to analyse should be inserted in the KNIME workspace, use the Explorer browse to select the folder containing the video. Alternatively, you can remove this node and leave a List node (without variable). 3. The workflow creates a folder with the same name as the video file analysed that contains the stack of images generated. After the analysis they should be removed to save disk space!4. In the wrapped metanode "Frequency analysis" the frame rate can be configure and should be the same for the ffmpeg program (metanode in the green area).5. Browse to select the folder containing the videos to analyse using the Explorer Browser node. 6. Adjust the threshold if necessary.7. Execute the "Loop end" node.Note: For manual analysis of tail contractions use the image viewer node and "manual check of frequency" metanode. The interactive Segmentation view allows to inspect if labels were correctly identify for each embryo.Tutorial on how to use the workflow coming soon...Please knowledge the workflow creation to: Dr. Stefan Scholz (Helmholtz Center for Environmental Research, UFZ, Leipzig).Dr. Elisabet Teixidó (University of Barcelona, Barcelona).Associated publications (submitted):Ogungbemi A., Massei R., Teixido E., Scholz S., Küster E. Optimization of the spontaneous tail coiling test for fast assessment of neurotoxic effects in the zebrafish embryo using an automated workflow in KNIME®. Neurotoxicology and teratology. Teixidó E., Klüver N., Ogungbemi A., Küster E., Scholz S. Evaluation of neurotoxic effects in zebrafish embryos by automatic measurement of early motor behaviours. Neuromethods. Teixidó, Elisabet, Klüver, Nils, Ogungbemi, Afolarin, Küster, Eberhard, & Scholz, Stefan. (2020). KNIME workflows for the evaluation of neurotoxic effects in zebrafish embryos by automatic measurement of early motor behaviours [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3835947 Threshold can be modified in configuration of componentnode. Negative values increase white pixels values andpositive values increase black pixel values Consult R documentation for definition of variables:smoothing factor (spar): https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/smooth.splineThreshold and noise cut: https://www.rdocumentation.org/packages/dpcR/versions/0.5/topics/test_peaks OPTIONAL: workflow to combine all results from different video files Run temporary.bat file for ffmpegWrite temporary .bat fileNode 23Wait until execution of .bat file is completedWait until .bat fileis createdList all video fileson folderNode 114Be sure to fill the eggs!Node 121Node 134Node 414Output takes the same name for the xls fileNode 452Node 453Node 454Node 455Node 456Node 461Node 463Node 465Node 466Node 467Node 471Node 472Node 473OptionalNode 475Node 478Node 489Node 493Node 504Node 506Node 507Node 508Extract name fileNode 510Node 512Node 513Node 514Select directorycontaining all excel filesNode 516Node 519Node 521Node 522DEFINE NAME .xlsJoin the File number to the column containing Name of the filesNode 526Pixel differenc binner positionNode 528Node 531Node 533Node 553Execute to analyseall videos in folderNode 556Layout to relateName of excel files to chemical concentration or treatmentNode 564Node 565optional for testingNode 577Node 578Node 579Node 580Node 1613Browse to select folder containingvideo filesCreates directory(may fail in caseof spaces in pathand file names)Creates path to .bat file External Tool CSV Writer(deprecated) List Files(deprecated) Wait... Wait... List Files(deprecated) Image Reader(Table) Global Thresholder ImageJ Macro Image SegmentFeatures XLS Sheet Appender(deprecated) XLS Writer(deprecated) Lag Column Image Calculator Global Thresholder Segment Cropper Joiner Joiner InteractiveSegmentation View Position binner Image Viewer Manual checkof frequency Sorter String Manipulation String To Number(deprecated) RowID Row Filter Median Filter Variable to TableRow (deprecated) Table Row to Variable(deprecated) Even or oddFrames filter Table Row to Variable(deprecated) Extract Variables(Data) Variable to TableRow (deprecated) Joiner Java Snippet(simple) RowID RowID XLS Reader(deprecated) XLS Reader(deprecated) List Files(deprecated) Table Row To VariableLoop Start (deprecated) Joiner Loop End Math Formula XLS Writer(deprecated) Joiner GroupBy Table Creator XLS Sheet Appender(deprecated) String Manipulation Image even orodd number Frequency analysis Mean frequency Loop End Table Row To VariableLoop Start (deprecated) Excel Reader (XLS)(deprecated) Joiner Check for error Row Filter Labeling toPNG Images Split CollectionColumn Joiner RowID Missing Value Explorer Browser Threshold Directory creation Path to ffmpeg Split labels

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Created by: sscholz
Created at: 2015-11-24
On NodePit since: 2020-05-10
Last update: 2024-04-23
Created with KNIME version: v4.3.0
Tags: zebrafishimage analysisR script

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