Jan
Since the CLI is probably the most straightforward way of using `atldld` I think we should have a dedicated section in the docs for it.
Currently, we only support downloading of ISH data, however, it might be useful to provide support for downloading of the standardized annotated atlases + reference (Nissl) volumes More context: https://help.brain-map.org/display/api/Atlas+Drawings+and+Ontologies
Might be actually really useful (potentially simplifying our pipelines). http://help.brain-map.org/display/api/Downloading+3-D+Expression+Grid+Data TODO: - [ ] Can one choose the resolution or is it fixed to 200 microns? - [ ] How...
We currently hardcode the respace to be (in microns). I guess because it is the canonical setup. ```python refspace = ( ("coronal", (0, 13200), ("transverse", (0, 8000), ("sagittal", (0, 11400),...
https://github.com/BlueBrain/Atlas-Download-Tools/blob/829206f9a2a21720bebc8830d51971315fccde27/tox.ini#L70-L83 It seems like the `todo` and `slow` markers are not used in the code anymore. Do you think we should keep them? Additionally, there are some tests that requires...
Whenever one calls `warp` the transformation needs to be computed from the displacements. https://github.com/BlueBrain/Atlas-Download-Tools/blob/60f0221916f4f9987a4728807be0b37934784cd0/src/atldld/base.py#L319 This operation requires `np.meshgrid` or `np.indices` and can be costly for big shapes. Anyway, the `DisplacementField`...
In `download_parallel_dataset` one can specify both the `downsample_ref` and `downsample_img` manually. However, it might be very useful to imply a reasonable `downsample_img` from the selected `downsample_ref` and the resolution of...
In theory, nothing prevents us from downloading + synchronizing the images in parallel.
In #40 a very simple logic of determining the refspace coordinate was implemented (inside of `download_dataset_parallel`). Namely: 1. Let the user choose `detection_xy=(x, y)` which is a fixed point in...