Biologic Images processing: Immunofluorescences

Question

[Francesco]

Hello everyone, I know I will have some microscope images to deal with in the context of a computational biology PhD on a developmental biology project. These Images are immunofluorescences acquired with an Opera Phoenix microscope. Therefore I was thinking that maybe there is some useful literature i can read to start thinking how to handle them. I would like specifically to read about:

1. How does cells change their morphology according to different cell fates
2. Methods to process microscopic images

Thank you in advance

[hq.huang11.6]

Hello, I also encountered the problem you mentioned above: methods of processing microscopic images (removal of background, false signals, etc...). If you've solved this problem and are happy to share your experience working with IF images, I'd be grateful for your help.

Answer 1

[bhumm]

I am by no means an image analysis expert but have done some work with it in the past. The majority of my experience is using ImageJ. Here is an article discussing the software in brief and has some helpful links: Quantitative Analysis of Histological Staining and Fluorescence Using ImageJ.

The majority of my colleagues used more sophisticated methods, namely MatLab and its various image processing toolboxes, specifically the image processing toolbox. Unfortunately, this software is not opensource and requires a license.

Finally, a PubMed search with the exact biological phenomena you are imaging and trying to analyze will be more fruitful than anything. There are many 'subfields' in imaging and really depends on what you are investigating (dot analysis, colocalization, FRET, etc.).

[hq.huang11.6]

Thank you, bhumm, your advice helps a lot!