CurveAlign Troubleshooting

Image Analysis
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#1

Hey ImageSC Community,

I am building a pipeline of sorts for analyzing whole slide histology images in QuPath but I am attempting to quantify the alignment of tendon/collagen as well. For this I have turned to CurveAlign but have found little resources to discus how to best go about using that software.

That being said I figured I would reach out here to see if anyone has used the software in the past and could supply any insight into the best practices for it.

At the moment, I have been using smaller regions of interest rather than the WSI. This ROI is about 3100 x 2144 pixels and looks like this:

image
image1340Ă—922 560 KB

I am running it at the 0.1 in the primary parameters as I have seen the best results from that so far. I haven’t attempted to use CT-FIRE yet but will look into it soon.

Overall I think CurveAlign does a fairly decent job quantifying alignment but I ran a test image of just cells and it returned a 20% alignment value which, in theory, should have 0 alignment as there was no tendon or collagen present.

Here is the link to CurveAlign’s website:

https://eliceirilab.org/software/curvealign/

Here is what the tool looks like:

image
image476Ă—950 22.3 KB

As always, Thank you for any insights!

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#2

Hi Avery,

I am the current lead developer of CurveAlign/CT-FIRE. Thank you for your questions. I have received your email about the use of CurveAlign and will reply to you shortly. We have been improving the user’s manual and the wiki webpage to answer all the typical questions that a user might have. You may also find our protocol helpful. The wiki page and the protocol information is listed below:

FAQ (CurveAlign) · uw-loci/curvelets Wiki · GitHub

Liu, Y., Keikhosravi, A., Mehta, G.S., Drifka, C.R., and Eliceiri, K.W. (2017). Methods for quantifying fibrillar collagen alignment. In Fibrosis: Methods and Protocols, L. Rittié, ed. (New York: Springer) (Protocol of using CurveAlign for alignment analysis)

Good luck,
Yuming

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