performing automatic registration for CLEM

Description

This is an example workflow of how to perform automatic registration by

- first detecting spots in both image using wavelet segmentation (with different scale according to the image scale)

- second using Ec-Clem autofinder to register both images

Click on a block to know more about a tool. Non referenced tools are non clickable.

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Workflow results

ICY batch pixel density measurement

Description

For each ROI, provides the ratio of pixels over a given threshold over the total number of pixels in the ROI.

ICY Median filter via ImageJ

Description

This protocol perform a median filter on the active sequence using the ImageJ rank filter plugin. Then, it converts the result back into Icy for display.

An example showing passing data between ICY and ImageJ using ImagePlus object. 

Track cell intensity

Description

Tracks a cell in a 2D video using active contours, and produces a list of ROI where intensity is measured and reported into a workbook. The cell must be first delineated with a ROI in the first image of the video.

need a thumbnail

Batch spot detection with custom output

Description

Download the protocol,use and modify in Icy. It permits to detect spot with wavelet spot detector block. Input : loop on a folder Outputs: excel, binary, and detection screenshot

has function
need a thumbnail

Find cells using nuclear and membrane fluorescence

Description

This protocol first extracts the cell nuclei from a given fluorescence channel (full labeling), and grows a contour from each nucleus to extract the cell edge in another fluorescence channel (membrane-labeling).