elgw / nd2tool Goto Github PK

Hi,

It would be amazing to have the nd2tool for mac.
But, it is not essential as we can use it on workstations.

Best,
Kaja

Show camera name in --info and put this information in the log file.

in meta-text, capture the line like

Camera Name: Andor Sona CSC-00633

and show that among the basic info.

Possibly also show the microscope model from the a line like

Microscope Settings:   Microscope: Ti2 Microscope

Hi
It would be practical to be able to choose which dimensions nd2tool splits images upon, for instance specifying "positions" but not "channels" to get individual multi-plane, multi-channel images in a memory-efficient way.
Thanks!
Q

. Add flag to split nd2 file into single 2D planes instead of the current 3D z-stacks.

. Add flag to format split data according to SpaceTx convention:

The stem of the tiles’ filenames must be <image_type>-f<fov_id>-r<round_label>-c<ch_label>-z<zplane_label>. The extension should be one of the formats supported by slicedimage.ImageFormat (tiff, png, npy). For example, the file nuclei-f0-r2-c3-z33.tiff would belong to the nuclei image, fov 0, round 2, channel 3, zplane 33.

The minimum time_types are "primary" (FISH imaging rounds) and "nuclei" (DAPI). We could attribute all FISH channels to "primary" with the different colors encoded into the -c variable.
It would be great to fetch metadata to create the physical coordinates csv file at the same time.

ref:
https://spacetx-starfish.readthedocs.io/en/latest/gallery/data_formatting/plot_format_structured_data.html#format-structured-data
https://spacetx-starfish.readthedocs.io/en/latest/help_and_reference/spacetx-format/SpaceTxFormat/index.html#sptx-format