I am trying to setup an automated pipeline to acquire images of individual neurites in a sample.
For this I am using the NIS elements software. I have both DAPI and Phalloidin available as stainings in my samples.
With the help of the General Analysis in the jobs feature I managed to exclude most cells without neurites.
However I do have the problem that often at higher cell density all cells and neurites are viewed as a single object.
This is a problem, because it does not allow me to filter based on elongation. While I could find tons of options for filtering out objects, I could not find any options on how to actually seperate objects.
Something I would like to do, is for example use the DAPI channel as an object breaker. I.e. dilate the nucleus and view everything starting on the other site of the nucleus as a new object.
I could not find any information about such operations, so I was wondering if anyone around here knows, if something like this is possible within the Nikon software.
If anyone has other suggestions on how to solve my problem, they are welcome as well.
I suppose in NIS-Elements it is not possible for filter out some objects, or as far as i know. Nevertheless, you could use ImageJ, since it provides vast opportunities for the image analysis.
Thank you for your answer Abhijeet Singh.
What I am trying to do is not to analyze my images, but to automatically let the microscope find the best possible fields of view, to image. To reduce the time I need to spend on the microscope myself and to reduce the personal bias of acquiring images.
NIS-Elements also is very good at excluding objects (based on intensity, circularity, elongation or size for example). It has enough features to filter for everything that I want, the only problem I am facing is that in many instances, such as in the image above, multiple cells are seen as a single object.
This object therefore will be excluded by the elongation filter, and the image is not acquired although it contains pretty much exactly what I am looking for.
On the other hand, if I do not use the elongation filter, the microscope is acquiring a lot of images that do not contain differentiated cells with neurites (which is what I am interested in seeing).
Cheers,
Max
- Badges
- Science method