Eduardo Hirata-Miyasaki

I am documenting here some of the questions that arose during the use of Viscy and the experience of running this during the DL@MBL course: I list them as tasks...

VS predictions should output the correct voxel_size/scale

1

One inconvenient step in the mantis analysis pipeline is having to go and remember to change the scale metadata on the virtually stained predictions. Is it possible to write the...

Fix converter for ndtiff using multicam

2

This PR fixes handling ndtiffs written with mutlicam. When using multicam, the datasets have an extra axis that needs to be parsed to reshape the output array.

iohub appending does not change or raise warning regarding datatype

1

The iohub `Position.append_channel()` function works great when the array to have a channel appended to shares the same `dtype`. In this case, we have some datasets stored as `dtype=np.uint16` and...

Cli rechunking

1

This was some of the code used during the DL course for rechunking #184

Contrast limit should follow the datatype of the dataset

1

Current datasets use the `channel_name` to determine the contrast limits of each dataset. For datasets that are not specified in the dictionary or do not match the `channel_name` string exactly...

Porting `create_empty_zarr` to iohub

4

This PR adds shrimPy utility functions relevant to iohub listed below: - `create_empty_zarr`: enables the creation of an empty zarr - `process_single_position`: function that can apply a czyx in czyx...

CLI or similar to change the channel names.

2

When processing iSIM + BF data, I have found the need for a function to rename channel names. So far, since I have had to do a crop, I rename...

Adding support for pyramids

4

This PR adds the support for pyramids to address #125. This modifies the `HCSDataloader()`

This PR is a temporary draft that includes segmentation functions (CZYX )for neuromast and cells. Until we figure out the imgprocessing repo and merge core multiprocessing utilites to iohub, I...