Fwd: Analyze labeled vesicles per cell

[Fco. Javier Diez Guerra]

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:  [phone]
e-mail: [hidden email]

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[Peter Mc]

Hi Javier;

The problem looks quite interested. I have been working in molecular image processing the last years and the technique (and the success) to use obviously depends a lot of you image so could yo show some example??

Best.

[Fco. Javier Diez Guerra]

Pedro,

Two sets of widefield stacks and confocal images (stained with dapi) are
available at the following link:

https://dl.dropboxusercontent.com/u/11107298/Analyze_vesicles.rar

These are raw images that have been scaled down to 50% to reduce weight.

Thanks

Javier


El 22/08/2015 a las 16:51, Peter Mc escribió:

> Hi Javier;
>
> The problem looks quite interested. I have been working in molecular image
> processing the last years and the technique (and the success) to use
> obviously depends a lot of you image so could yo show some example??
>
> Best.
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Fwd-Analyze-labeled-vesicles-per-cell-tp5014109p5014111.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Sean Burke]

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
[hidden email]

-----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:  [phone]
e-mail: [hidden email]

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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