elgw / nd2tool Goto Github PK
View Code? Open in Web Editor NEWConvert Nikon nd2 files to tiff
License: MIT License
Convert Nikon nd2 files to tiff
License: MIT License
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
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.