Help With Align Module



I have a group of microscopy images (beads in a flow chamber) which I want to align with respect to each other or a base image, but I do not want the beads to be considered while using the images in the align module. Is there a module using which I could selectively remove all the beads and then use the remainder image to align them using cross correlation. The images can be accessed at the following address

There are also some extraneous objects such as a water bubble which I would like to also disregard when aligning images. Can somebody help me with the align module.

Thanks in advance



I would recommend making a base image that will look like a template of your squares in the background (without the beads or water marks). For an example of this, you can try downloading the “Classified Colonies” example form the web page. In this example, a plate template is used to align yeast plates.



Thanks for the suggestion, but it seems like the module works pretty well on the given images. I have few more questions regarding the Align module

  1. I want to align the group of images with respect to a single image, but I am not sure how to do the batch processing. I have tried adding Align module based on the number of images I want to Align but not sure whether thats the right way to do it. Is it possible to program the module to pick the first image as the base image and align the remaining images in the folder?

  2. After it has aligned the images, it colors them like green, blue etc. It helps see what has happened to the image and how it is aligned but is it possible to get those images without color if we want to further process them.

Thanks a lot for the help



So, to answer your questions…

  1. Yes, you can use the LoadSingleImage module to load your ‘template’ image. The LoadSingleImage module will only load that particular image once and use it for all cycles. This will solve the problem of needing to load the same image for the alignment step.

2)The coloring is only for the figure window. The idea is to show the user a before and after of the alignment. The newly aligned images are stored and can easily be saved or processed after the Align module by using the SaveImages module.

Hope this helps!