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SpotDetectorScale2and3-inBatch

by IcyLyd / IcyLyd

This protocol allows detecting spots using wavelet spots detector plugin.
It combines the wavelets spot detector for scale 2 and 3 and export the spots localization in a single ROI over the picture to visualize them on a single layer.

In contrast with the Spot detector scale 2 and 3 protocol, this one allows functionning on a folder to make batch analysis. ROI statistics is exported in a result folder at the same hierarchical level. All the results concerning the different file image are merge in one single excel file.

version 1 (last version):

Download to use and modify in Icy. How do I use protocols ? A Problem ? ask the community.
Changelog for this version: initial version

Documentation

This protocol is an example to use file batch analysis on a folder.

In Javascript bloc #12, it creates a results folder at the same hierarchical level than the Image folder selected.

The result Folder name is indexed with the date of the analysis.

CreateResultFolder

This folder contain a single excel file containg all the parameters available in ROI statitics bloc (#15) concerning the detected spots, that mean :

Contour (ie perimeter for 2D, External envelop for 3D)
Interior (ie surface in 2D, volume in 3D)
Sphericity (%)
Roudness (%)
Convexity (%)
Max. Feret diam.
Ellipse (a)
Ellipse (b)
Ellipse (c)
Elongation ratio
Flatness ratio (3D)
And Intensity of the ROI in the different channels of the picture.

ExcelExport.png

The workbook to file mode use the "merge sheets" mode allowing to append data from different picture (here Hela-Cells-01.tif and Hela-Cells-01.tif) in the same file.

MergeFile.png

 The workbook to file mode use the "merge sheets" mode allowing to append data from different picture (here Hela-Cells-01.tif and Hela-Cells-01.tif) in the same file.

 



Icy protocol publication Id : Y6M2S5