Upload
others
View
41
Download
5
Embed Size (px)
Citation preview
Coloc-TesselerInstallation guide & Manual
By F. Levet & JB. Sibarita
Team Quantitative Imaging of the Cell
Interdisciplinary Institute for Neuroscience
CNRS UMR5297, Univ. Bordeaux
Installation (1/2)
• Need a PC with Windows (7/10) and OpenGL installed
• Launch « Coloc_Tesseler_Setup.msi »
• Select installation directory
Installation (2/2)
• Installation folder contains executable, icons, fonts, DLLs files anddataset examples
• Unzip « Datasets.zip » example files (in Datasets directory). This willcreate three sub-directories (Experimental, Simulations_2D andSimulations_3D)
Coloc-Tesseler Quick start (1/3)
• Launch « Coloc-Tesseler.exe »
• 2 windows will pop-up• A Console (for application messages)
• A fullscreen Viewer
Coloc-Tesseler Quick start (2/3)
• Single-molecule data are in csv format (Thunderstorm)
• To open single-molecule data:• Click on the open icon
• Choose « Open Localization File » to open a single file
• Choose « Open Dir » to open all files in a given folder
• Choose « Open Dir »• Go to Coloc-Tesseler\Datasets• Single click on « Simulations_2D »• Click on « Choose »
Coloc-Tesseler Quick start (1/3)
• Six datasets are opened (corresponding to three 2-colors simulations)
Interaction panel
Coloc-Tesseler GUI – Misc. Tab (1/1)
• Click on the background color to change it
Coloc-Tesseler GUI – Localizations Tab (1/2)
• Single-molecule detections can be displayed by checking the« Display » check-boxes
Coloc-Tesseler GUI – Localizations Tab (2/2)
• Change parameters of the histogram by middle-cliking on it
• Click on the color button for changing the LUT
• Check the parameter you want to change and enter the new value
Coloc-Tesseler GUI – Toolbar (1/2)
• Zoom by clicking on the glass icon
• The zoom is continuous: hold the mouse clicked and move the mouseup or down to zoom-in or zoom-out
• Click on the hand to move laterally in the data
Coloc-Tesseler GUI – Toolbar (2/2)
• Click on the « Colocalization » Icon to bind the 2-colors of a dataset
• Check « All 2-colors datasets » to bind all the opened dataset by 2
• Check « One 2-colors datasets » to choose the 2 datasets to be bind
• Click on « Ok »
Coloc-Tesseler GUI (1/1)
• Three 2-colors datasets are created• First color is displayed in red
• Second color is displayed in green
• Voronoï diagrams for both colors are created
Coloc-Tesseler GUI – Colocalization Tab (1/4)
• Coloc-Tesseler automatically computes the Spearman/Manderscoefficients and classifies the localizations• At this stage, Coloc-Tesseler uses a threshold of 1
• Interaction is possible through the « Colocalization » tab
Voronoï scatterplot
Display options
Threshold options
Colocalization values
Coloc-Tesseler GUI – Colocalization Tab (2/4)
• (Un)check the corresponding check-boxes to (not) display theclassified localizations (Color A & B), the classification backgroundclass (black localizations), the original localizations and the Voronoïdiagrams
1
2
3
1 2 3
1 + 2 + 3
Coloc-Tesseler GUI – Colocalization Tab (3/4)
• Check « log » for log display of the Voronoï scatterplot
• You can change the grid size of the color map
Coloc-Tesseler GUI – Colocalization Tab (4/4)
• Modification of the thresholds can be done in two ways1. Direct click inside the scatterplot
2. Direct modifications of the thresholds
• The use of one of these methods will update the other
1
2
Coloc-Tesseler GUI – ROIs (1/2)
• Click on the « Define ROI » to create ROIs• Line, circle, square, triangle & polyline are possibles
• ROIs can be saved, loaded, discarded and are accessible in the ROI manager
Coloc-Tesseler GUI – ROIs (1/2)
• Colocalization analysis is automatically performed on ROIs
Coloc-Tesseler GUI (1/1)
• Click on the « Close All » to close all datasets
Coloc-Tesseler – Experimental dataset (1/1)
• Open directory « Coloc-Tesseler\Datasets\Experimental »
• Click on the « Colocalization » Icon with « All 2-colors Datasets » checked
• Load ROI file « spinesROIs.txt » for colocalization analysis on selectedsynapses
Coloc-Tesseler – 3D simulations (1/2)
• Open directory « Coloc-Tesseler\Datasets\Experimental »
• Four localization files are opened (two 2-colors datasets)• 1st condition: Full colocalization (distance between 2-colors clusters is 0 nm)
• 2nd condition: Partial colocalization (distance between 2-colors clusters is 50 nm)
Coloc-Tesseler – 3D simulations (2/2)
• 3D Voronoï diagrams are projected on a 2D camera• Difficult to understand uncheck the Voronoï diagrams rendering
By being 2D, ROIs shouldnot be used with 3D
datasets