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flevet / PoCA

https://poca-smlm.github.io/
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Export data for publication #6

Open Brito-Alarcon opened 6 months ago

Brito-Alarcon commented 6 months ago

Hi Florian, big fan of your tesselation works in the SMLM space!

I will use POCA for the final analysis, but I am having difficulties for the following things:

  1. Can I use other LUTs and/or colormaps? I am looking for something friendly for color-blind people.
  2. How do you save the image? I use Ctrl + S, which saves as an SVG file, but I can not work with it directly. At first, I tried Inkscape with no success, with Adobe Illustrator asking for a validation. Have to convert the file to PDF and then to SVG again with https://cloudconvert.com/. Is this your normal workflow for exporting images from POCA? How do you do it?
  3. Can you save the visualized file as an image and not as an SVG?

Thanks!

flevet commented 5 months ago

Hi,

Thanks and sorry for the delayed answer! About your questions:

  1. As of right now it is not possible for users to add customized LUT. I thought about it but did not have the time yet to add the feature. You can always give me the LUT in order that I add it. The format would be the different colors you need between 0 and 1. If a LUT has two colors ([0, rgb(255,0,0)] -> [1, rgb(0,0,255)]) ie red at position 0 and blue at position 1, the LUT will be a gradient from red to blue. The LUT can be composed of any number of [point,color] between 0 and 1.
  2. When I'm saving the 2D localizations as svg, I'm using Inkscape. It is only possible for a small number of locs (few hundreds max) as Inkscape is not able to handle thousands of individual objects. I tend to ungroup all the objects and then change their sizes depending on my needs.
  3. When I want images, I do a simple screenshot of PoCA. Not the best solution but I doubt I will have time to do an offscreen rendering saved as an image.

Cheers