How to adjust proper resolution?

[Marcin Głogowski]

Hello, I was not able to find documentation how to adjust pixel/micrometer resolution so

I used the old documentation for Microbe Tracker that can be found here https://microbetracker.org/help/helpMicrobeTrackerParameters.htm

The problem is that I don't have idea which resolution should I take (picture resolution? screen resolution? camera resolution?) to be able to see bacteria with proper sizes.

I used scaleFactor parameter and cellwidth without success.

The problem is that under microscope my bacteria size is 3 micrometer and under OutFti application.

I'm attaching to this post Serratia marcescens (length 1.5 - 3 um) picture taken be my microscope. Magnification 100x with 5MP camera (pixel size 2.2 micron).

Thank you for any advices

[Oufti]

Hi Marcin,

You should be able to segment cells using Oufti, without having to worry too much about the resolution of your images. The scaleFactor is a parameter that is no longer used in Oufti, and is a remnant of older segmentations algorithms in microbeTracker. The two main parameters that are somewhat resolution-sensitive are "areaMin" and "cellWidth". Both are expressed in terms of pixels and represent a lower bound on cell size and an initial guess for the width of cells, respectively. 

My recommendation to get the segmentation working would be to review the parameters and their descriptions in the Oufti web page and focus on the segmentation module to get the best segmented image possible. From there, it might be most helpful to play with the parameters on the provided example data sets and see how the cell meshes are affected. In general, I would adjust one parameter at a time and go from there. Unfortunately, we are unable to tune parameters for all users.

Thanks for using Oufti!

Oufti-team

Op maandag 30 augustus 2021 om 17:38:01 UTC+2 schreef marcin.toma...@gmail.com: