Aafke Gros
@aafkegros.bsky.social
Check out Microscopy Nodes for handling microscopy data in Blender! Now loading .tif and OME-Zarr with big volume support :)
she/her | IPA: ˈafkə ɡrɔs
she/her | IPA: ˈafkə ɡrɔs
And it also works in 2D 😁 Here we extract a circular projection instead of a spherical, and apply a 1D Fourier transform.
Here we can see how the channel distributions all align in the projection after we optically activate Rac1 in one part of the cell. 💡
With @jpassmore.bsky.social , Lukas Kapitein
Here we can see how the channel distributions all align in the projection after we optically activate Rac1 in one part of the cell. 💡
With @jpassmore.bsky.social , Lukas Kapitein
January 30, 2025 at 10:11 AM
And it also works in 2D 😁 Here we extract a circular projection instead of a spherical, and apply a 1D Fourier transform.
Here we can see how the channel distributions all align in the projection after we optically activate Rac1 in one part of the cell. 💡
With @jpassmore.bsky.social , Lukas Kapitein
Here we can see how the channel distributions all align in the projection after we optically activate Rac1 in one part of the cell. 💡
With @jpassmore.bsky.social , Lukas Kapitein
We then use spherical harmonics decomposition to quantify the variance in the spherical signal per angular wavelength.
This gives us a metric that shows how detailed the features in the spherical map are, giving a rotation-invariant quantification of distribution.
This gives us a metric that shows how detailed the features in the spherical map are, giving a rotation-invariant quantification of distribution.
January 30, 2025 at 10:11 AM
We then use spherical harmonics decomposition to quantify the variance in the spherical signal per angular wavelength.
This gives us a metric that shows how detailed the features in the spherical map are, giving a rotation-invariant quantification of distribution.
This gives us a metric that shows how detailed the features in the spherical map are, giving a rotation-invariant quantification of distribution.
To quantify a segmented microscopy object, we project this to a spherical mean map.
This video is made with @blender3d.bsky.social geometry nodes and Microscopy Nodes, allowing the microscopy and method illustration in the same video :D
This video is made with @blender3d.bsky.social geometry nodes and Microscopy Nodes, allowing the microscopy and method illustration in the same video :D
January 30, 2025 at 10:11 AM
To quantify a segmented microscopy object, we project this to a spherical mean map.
This video is made with @blender3d.bsky.social geometry nodes and Microscopy Nodes, allowing the microscopy and method illustration in the same video :D
This video is made with @blender3d.bsky.social geometry nodes and Microscopy Nodes, allowing the microscopy and method illustration in the same video :D
Now out in PLOS CB: Spherical Texture extraction! doi.org/10.1371/jour...
This method quantifies the intensity distribution in microscopy objects, and is implemented parameter-free in @ilastik-team.bsky.social object classification!
We show applications in cells, C. elegans and Drosophila! 😁
This method quantifies the intensity distribution in microscopy objects, and is implemented parameter-free in @ilastik-team.bsky.social object classification!
We show applications in cells, C. elegans and Drosophila! 😁
January 30, 2025 at 10:11 AM
Now out in PLOS CB: Spherical Texture extraction! doi.org/10.1371/jour...
This method quantifies the intensity distribution in microscopy objects, and is implemented parameter-free in @ilastik-team.bsky.social object classification!
We show applications in cells, C. elegans and Drosophila! 😁
This method quantifies the intensity distribution in microscopy objects, and is implemented parameter-free in @ilastik-team.bsky.social object classification!
We show applications in cells, C. elegans and Drosophila! 😁
To learn more, please check out my youtube tutorials at www.youtube.com/@oanegros which shows, among others, how to make this video!
The data here is a dinoflagellate from Mocaer et al. 2023, hosted publicly at EMPIAR-11399 (also shown in the first post here).
The data here is a dinoflagellate from Mocaer et al. 2023, hosted publicly at EMPIAR-11399 (also shown in the first post here).
January 15, 2025 at 1:39 PM
To learn more, please check out my youtube tutorials at www.youtube.com/@oanegros which shows, among others, how to make this video!
The data here is a dinoflagellate from Mocaer et al. 2023, hosted publicly at EMPIAR-11399 (also shown in the first post here).
The data here is a dinoflagellate from Mocaer et al. 2023, hosted publicly at EMPIAR-11399 (also shown in the first post here).
Microscopy Nodes loads data from a @zarr.dev bucket, making it easy to use open data archives that host Zarr data!
This is a mitotic cell from Walther et al. 2018, that's hosted publicly on the Image Data Resource 😱
This is a mitotic cell from Walther et al. 2018, that's hosted publicly on the Image Data Resource 😱
January 15, 2025 at 1:39 PM
Microscopy Nodes loads data from a @zarr.dev bucket, making it easy to use open data archives that host Zarr data!
This is a mitotic cell from Walther et al. 2018, that's hosted publicly on the Image Data Resource 😱
This is a mitotic cell from Walther et al. 2018, that's hosted publicly on the Image Data Resource 😱
With Microscopy Nodes, you can play with large volumes (this ExM dataset from Granita Lokaj is 49 GB total) and integrate this with all the cool tools in Blender, such as this #geonodes model of the centriole, made by @banterlegroup.bsky.social !
January 15, 2025 at 1:39 PM
With Microscopy Nodes, you can play with large volumes (this ExM dataset from Granita Lokaj is 49 GB total) and integrate this with all the cool tools in Blender, such as this #geonodes model of the centriole, made by @banterlegroup.bsky.social !
And with OME-Zarr we can easily load data from public databases on the internet, such as the Bioimage Archive or IDR. Here is a beautiful mitosis dataset from Walther et al. (2018), hosted at uk1s3.embassy.ebi.ac.uk/idr/zarr/v0....
October 21, 2024 at 8:30 AM
And with OME-Zarr we can easily load data from public databases on the internet, such as the Bioimage Archive or IDR. Here is a beautiful mitosis dataset from Walther et al. (2018), hosted at uk1s3.embassy.ebi.ac.uk/idr/zarr/v0....