Comments (2)
Thanks for raising the questions. I assume your data is stored in a csv file?
Ncem for custom data depends on AnnData as an input data object. More information on how to store your data as an AnnData ibject can be found in the following three documentations:
- AnnData documentation: https://anndata.readthedocs.io/en/latest/
- Scanpy documentation: https://scanpy.readthedocs.io/en/stable/
- Squidpy documentation: https://squidpy.readthedocs.io/en/stable/#
I hope this helps and please reach out again in case of further questions
from ncem.
Hello @AnnaChristina Thank you for taking the time to respond to my comments. I am using CODEX output and have segmented it using Qpath. The file includes x and y coordinates with gene/protein expression matrices for annotated markers in CSV format. I was wondering if you could provide me with more information about your analysis of the CODEX dataset. Specifically, I am curious about what type of output you used from CODEX itself or from other software. Additionally, I would like to know which segmentation pipeline you used.
The reason for my inquiry is that I want to ensure that I am following the correct pipeline to generate my results. Any information or guidance you could provide on this matter would be greatly appreciated.
Thank you for your help.
from ncem.
Related Issues (20)
- How to run NCEM for own spatial data? HOT 2
- Error while loading custom data in NCEM HOT 2
- Where can I find the cell_metadata.csv file for MERFISH brain data in merfish_brain.ipynb? HOT 1
- ncem - python 3.9 HOT 1
- Use Tangram mapped visium for ncem HOT 10
- compatibility with 10x visium HOT 4
- Issue installing ncem on macOS
- Supporting jinja2>=3.0.3 HOT 1
- Input to the "interaction linear model" HOT 2
- QuestionInternalError: Graph execution error: HOT 1
- Naive Question
- LinAlgError: SVD did not converge HOT 2
- Work with 10X Visium Estimator
- cannot get the grid search results HOT 1
- Almost zero documentation for the training modules API HOT 3
- Trouble installing on python 3.10 HOT 5
- Question about r2 values
- Update required: extend_formula_ncem
- 1877 del celldata.uns["spatial"] - error
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from ncem.