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EIN-lab / CHIPS

CHIPS, or Cellular and Hemodynamic Image Processing Suite, is an open-source MATLAB toolbox designed to analyse functional images of cells and blood vessels, primarily from two-photon microscopy. Please see the README file, which is displayed at the bottom of this page, for more information.
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Allow rotation of CompositeImgs for use in FrameScan() (Orig: Calculating diameter and velocity from non-parallel to scan vessels) #9

Open pbl007 opened 3 years ago

pbl007 commented 3 years ago

Hi. Does CHIP contain algs implementations for measuring velocity and / or diameter for vessels with arbitrary angles withe respect to linescan direction (i.e. for vessels that are not parallel to the lines)? Thanks! Pablo

kferrari commented 3 years ago

Hi Pablo I don't think CHIPS can handle arbitrary angles, as there is no way of determining the angle at which the line scan was drawn in respect to the vessel. Line scans are expected to be drawn parallel to the vessel and at the center for velocity calculations and at a 90° angle for diameter calculations. But, maybe I'm missing something? Could you give some more information about what you're trying to achieve? Thanks, Kim

pbl007 commented 3 years ago

Hi Kim, thanks again for making CHIPS available for all! How about allowing the user to draw a line *along the vessel so one can then rotate the image with the specific angle prior to processing. One will need also to account for this angle when reporting velocity but no further changes will be needed for diameter. How does it sound? Doable?

kferrari commented 3 years ago

Sorry for asking, are we still talking about line scans or rather about frame scans? For frame scans this might be possible. I'm not sure how dependent the algorithm is on pixel time - or rather between-pixel time. As it stands now, I don't think we (our lab) can implement this in a timely fashion. Once I'm sure what you mean, I'll open a separate issue with the feature request and I'll think about possible ways to implement it.

pbl007 commented 3 years ago

Indeed frame scans only. Will be great to have it implemented in the near future to make CHIPS our tool for years to follow (I am hoping this should be the community standard tool).

kferrari commented 3 years ago

Thank you for the kind words :-)

I think the shortest and cleanest way to implement this would lead via CompositeImg, as this class was designed to subset image regions. We'll have to find a way to rotate and transform the metadata where necessary. I'll change the title of the issue to leave communication here for reference.

pbl007 commented 3 years ago

Hi Kim

hope all is good on your side.

I would love to get CHIPS as our tool for blood flow analysis in the lab but I am facing severe issues (just opened one in the GitHub). I can go head an open more issues on the repo but before doing so I wanted to know if you (or someone else) will be maintaining the repo. Could you be kind to let me know and if the answer is positive then try to help us to get up and running w/CHIPS?

Thanks a lot in advance, Pablo

Pablo Blinder, PhD http://pblab.tau.ac.il http://pblab.tau.ac.il/en Neurobiology, Biochemistry and Biophysics School, George S. Wise Faculty of Life Sciences, and Sagol School for Neuroscience, Tel Aviv University

On May 18, 2021, at 17:07, Kim Ferrari @.**@.>> wrote:

Thank you for the kind words :-)

I think the shortest and cleanest way to implement this would lead via CompositeImg, as this class was designed to subset image regions. We'll have to find a way to rotate and transform the metadata where necessary. I'll change the title of the issue to leave communication here for reference.

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kferrari commented 3 years ago

Hi Pablo I'm sorry for seemingly loosing sight of your issues. There's a lot going on at the moment and I don't have the time to do major maintenance or updates. This might change in the future, but for now your safest bet would be to fork a copy of this repo and do the changes yourself. I can try to assist you with tips and ideas, but I'm afraid we don't have the means to implement your requests at the moment.