Identifying different parts of a single spore

I’ve been working on a project identifying conidia (spores) in photos of a wash of C. Heterostrophus under a 10x microscope with substantial success. My next task is to take a similar wash and use it to quantify the portion of conidia that have begun to germinate. This involves measuring a small strand that has begun to grow out of the end of each conidia (see photo) and comparing its dimensions to the size of the conidia.

I have attached the identified objects from my original pipeline. As you can see, there is no problem in recognizing the strands growing out of conidia. I was wondering if anyone has tips for differentiating the conidia from the new growth. As yet, I have not thought of a good way to do this.


I’m attaching a pipeline which is a first attempt at distinguishing the spores from the strands and computing measurements. Please see the annotations at the top of the module to see my thought process. This is by no means a final solution, so some tweaking is probably required to optimize the results for your images.

Hope this helps!
2011_06_07.cp (12.9 KB)

Thanks so much. This is just what I needed to get started.

Another question, if you don’t mind:

The pipeline you gave me is working quite well, with a few modifications. The problem I am having is in taking measurements. In order to determine germination, it is necessary to consider only the length (or area in this case) of the longest strand. The relate objects module calculates the mean area of child objects, which is fine if a spore has only one strand. However, spores with two strands, such as the spore in the bottom left of the first image in this thread, return inaccurate results; the two strands are considered to be one child object and the area measurement is much larger than it should be. If these two strands could be considered separate child objects (is it possible to have more than one child per parent?), then the mean would give a reasonable measurement from which to determine germination. Ideally, though, I would like two separate strands on opposite ends of a single spore to be considered separate objects and then look at the maximum child area per parent. Is there any way to do this? I have attached my modified pipeline for reference; the load images module will need to be modified.

2011_06_14.cp (13.1 KB)

So I figured out part of my question: I was able to separate two strands on either end of a single spore by converting object to image and re-identifying strands. However, I would still like to know the bit about finding the maximum child area per parent rather than the mean child area per parent. Attached is my latest pipeline.

2011_06_15.cp (16.4 KB)

Hi Mike,

I think in this case, you will want to use MeasureObjectSizeShape to measure the strands and then use FilterObjects to filter the strands using “Maximal per object” as the filtering method, the skeletonized strands as the children, and the expanded spore objects as the parents. The result should be one strand (the one with the largest area) per spore remaining.


Thanks, Mark. This worked perfectly.