allow to use other image types (than phase contrast) for tracking

[julou]

this has come over and over in emails but never made it as an issue (probably because not required for the first method paper and not a minor request…)

because MoMA produces a set of nested segmentations hypotheses and then handle them as a graph, it should in principle be possible to generate this segmentations hypotheses from other types of images such as fluorescence (uniform cytoplasm tagging) or more sensitive phase reconstructed images (such as correlation images).

Importantly, this should be designed as far as possible such that users can support new image types by themselves (by defining a config file and e.g. training a classifier)…

This should also help improving the following:

• more precise segment length estimation
• reduce the need for manual curation (because e.g. fluorescence images are supposed to be less error-prone)

[erikvannimwegen]

Explanation:
This is really a very important issue. There is almost nobody in the community that uses phase contrast to segment images of bacterial cells. Almost everybody makes sure that all cells are fluorescent and then use the fluorescence image to segment the cells.
Now, it is of course very nice that MoMA can segment on phase contrast (meaning that you can even use cells from the wild that have no fluorescence in them) but in many situations the cells that one is tracking ARE in fact already fluorescent. In those cases, it will be very hard to understand to people in the field that MoMA does NOT allow using the fluorescence to segment the images. Not using fluorescence for segmenting when you have it is like trying to do things with your hands tied behind your back.
This is because the cells are much more easily distinguishable in the fluorescence image.
As an important side effect, I note that our cell size estimation is currently still very crude and not really satisfactory (even with the refinement that we coded). Using fluorescence images we would likely get significantly better size estimates and this is another reason why this is very attractive.
So this is something that we really want to see implemented at some point.
Would be good to get a sense of how hard/how much work you think this is.

[fjug]

I assume that data obtained with an ubiquitously expressed fluorescence signal would just work. I'd be happy to give it a try in case such datasets are readily available.

[erikvannimwegen]

Great! We will get you this very soon.

[julou]

Yes, this is really great!
btw how realistic is it to allow users to customise MoMA to new image types by themselves?

[julou]

So, I gave a quick look at the data we already shared. The following datasets have uniform cytoplasmic fluorescence on channel 2:

http://swissregulon.unibas.ch/video/Missing_hypothesis/20150630_pos0_GL05
http://swissregulon.unibas.ch/video/Missing_hypothesis/20150630_pos1_GL08
http://swissregulon.unibas.ch/video/Missing_hypothesis/20150630_pos2_GL09
http://swissregulon.unibas.ch/video/Solutions/20150624_pos0_GL02
http://swissregulon.unibas.ch/video/Solutions/20150624_pos0_GL06
http://swissregulon.unibas.ch/video/Solutions/20150624_pos1_GL01
http://swissregulon.unibas.ch/video/Solutions/20150624_pos1_GL02
http://swissregulon.unibas.ch/video/20150630_pos1_GL13

if you need more GLs:
http://swissregulon.unibas.ch/video/20150624_pos0/output

Importantly, one GL with uniform fluorescence at lower illumination (hence lower signal to noise ratio) is available here (I could share more if you need):
http://swissregulon.unibas.ch/video/20160805_sent/20160427_pos0_GL04.tar.gz

[julou]

as mentioned above, another type of images that would be very interesting to use for us is correlation images.

We prepared a small dataset (http://swissregulon.unibas.ch/video/20160917_sent/20160914_Pos0.tar.gz) with the following channels:

1. phase contrast
2. uniform fluorescence
3. correlation images

It would be very interesting if MoMA was able to use any of these image type for tracking. Please let me know if you need more info / longer datasets…
Once this is implemented, we'll be able to compare the accuracy with the 3 different types of images.

NB: this has lower priority than being able to use fluorescence images for tracking, but still correlation images should be more reliable than standard phase contrast.
And having more than 2 types of images might help thinking of a more modular way to handle these different types…

[julou]

also if it becomes possible to use different image types, it would be very convenient to be able to tell MoMA which channel of the image dataset should be used for tracking (cf #2 (comment)).