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general > RE: Ability to use custom atlas labels
Aug 6, 2024 11:08 AM | Gergely Csucs
RE: Ability to use custom atlas labels
Hi Aaron,
I tried using a modified python code to read the flat file, however, the output is a low-res PNG. What would I need to do in order to get a high-res PNG similar to what is the final output images using NUTIL?
Nutil gets that low-resolution image too, then scales it up to
the desired resolution (of the image coming from Ilastik -
typically). ImageJ/Fiji can do this too: Image menu, "Scale...",
then type the needed resolution and set Interpolation to
None.
I am specifically interested in extracting the distinct cerebellar nuclei. If each of these nuclei have different colors, I can use fiji to extract ROI based on color information. However, currently the labeling in the final output of NUTIL yields the same color for all cerebellar nuclei.
Yes, this issue comes up from time to time. A workaround is
provided at https://www.nesys.uio.no/VisuAlign/relab... - it's a
small tool that creates a label file with distinct colors (not
necessarily for the human eye, but for programs like Fiji), that
can be used with VisuAlign.
I hope this helps.
Best regards,
Gergely
Threaded View
| Title | Author | Date |
|---|---|---|
| Austen Casey | May 14, 2023 | |
| Gergely Csucs | May 15, 2023 | |
| Austen Casey | Jun 16, 2023 | |
| Austen Casey | Jun 17, 2023 | |
| Gergely Csucs | Jun 20, 2023 | |
| Aaron Sathyanesan | Aug 5, 2024 | |
| Gergely Csucs | Aug 6, 2024 | |
| Aaron Sathyanesan | Aug 20, 2024 | |