Doug Shepherd

Two questions about converting larger than memory ND data into ome-zarr

4

Hi all, Thanks for the hard work on this package and overall on ome-ngff. We are very excited to learn that Dask arrays are now supported! We have 4D data...

Fusion of single-view data?

7

Hi all, Super exciting to find this project! We are acquiring large light sheet data sets using a high NA oblique plane microscope ([publication](https://elifesciences.org/articles/57681)). We normally use BigStitcher to stitch...

Reading in non-CZI data

1

We also have a second, but separate question. We typically save our data as TIFFs and then convert to the BigDataViewer (BDV) H5 format, using [npy2bdv](https://github.com/nvladimus/npy2bdv). Since we can read...

Custom engine with sequenced acquisitions

6

Hi all, We are finally diving into sub-classing the acquisition engine and the new approaches for on-the-fly and file saving. I think with all of these tools (again, thank you...

Dask kernel dies when fusing large images

12

We've been running into an issue where our Ubuntu 22.04 machine kills Dask when trying to fuse large images. We seem to have temporarily solved it by stopping the out-of-memory...

feat: more efficient proximal total variation operator

4

Implement TV operator found in: Kamilov, Ulugbek S. "[A parallel proximal algorithm for anisotropic total variation minimization.](https://doi.org/10.1109/TIP.2016.2629449)" IEEE Transactions on Image Processing 26.2 (2016): 539-548.

Add iterative AO optimization feature to GUI.

Switch to asyncio tensorstore w/ zarr v3 compliant store. Moved metadata to `json`, but need to check into how to do this to match a `.zattrs`

Use with high axial sampling 3D data?

1

Congrats on the paper being out! The comparison to existing methods is interesting and we certainly see an inflation of cell numbers at times using Baysor on our data. We...

Add weak scattering reconstruction using our FISTA opimitzer