Posted by
Sean Burke on
Aug 24, 2015; 4:29pm
URL: http://imagej.273.s1.nabble.com/Fwd-Analyze-labeled-vesicles-per-cell-tp5014109p5014131.html
Hello Javier,
I had some luck with segmentation and analysis of your images using the cellular/vesicle staining channel alone. I used ImageJ to split the stacks and CellProfiler to do an illumination correction on the cellular channel as well as a texture enhancement of the corrected images to better visualize the vesicles. The images were then segmented accordingly and I exported the data for further visualization and analysis in FCS Express Image cytometry. I have uploaded the CellProfiler project, Output of the exported data, the FCS Express Image Cytometry Layout, and screenshot of some basic results at:
https://www.dropbox.com/s/wzafmtul58vyw1l/VesiclesCellProfilerFCSExpress.zip?dl=0. If you have any questions about this just shoot me a note.
You should be able to modify the pipeline to further refine the segmentation and automate the process.
Regards,
Sean Burke
-----------------------------
Sean Burke
Product Manager
De Novo Software
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-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Fco. Javier Diez Guerra
Sent: Saturday, August 22, 2015 6:48 AM
To:
[hidden email]
Subject: Fwd: Analyze labeled vesicles per cell
Hi,
We want to automate the generation of ROIs that fit into the area occupied by individual cells cultured on coverslips (HeLa, MDCK, COS7, etc). The purpose is to analyze the distribution of labeled vesicles (number, size, etc.) in a cell to cell basis.
I will appreciate any suggestion regarding suitable plasma membrane stains that can be used in fixed cells to outline their contours and help with the initial thresholding and segmentaton.
In addition, I will be grateful to listen to your comments on the most appropriate method (public macro or plugin) to automate this task. We have tried the Mosaic Suite for ImageJ/Fiji and also Cell Profiler in coverslips which were also counterstained with DAPI (to act as a seed), with very limited success.
Thanks
--
Fco. Javier Díez Guerra, PhD
Profesor Titular
Centro de Biología Molecular Severo Ochoa C/ Nicolás Cabrera, 1 Universidad Autónoma Ctra Colmenar Viejo Km 15 Cantoblanco, 28049 Madrid SPAIN
phone: +34 91 196 4612
e-mail:
[hidden email]
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