cytomining/CytoDataFrame

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An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.

Stars: 13
Forks: 2
Open beginner issues: 0
Indexed issues: 33
Avg merge: 1d 16h
Merged PRs (30d): 3

Dominant language: Python
License: BSD-3-Clause
Last GitHub push: Sep 3, 2026
Latest indexed: Sep 15, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

Open All

33 open issues indexed

Enable compatibility with multiple dataframe types Open

enhancement

cytomining/CytoDataFrame#88 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Provide customization options for bounding boxes with `CytoDataFrame` image display Open

enhancement

cytomining/CytoDataFrame#27 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Update docsite to use sphinx-multiversion (post initial release) Open

documentation enhancement

cytomining/CytoDataFrame#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add Python 3.13 compatibility Open

enhancement

cytomining/CytoDataFrame#20 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
NF1 dataset: image issues Open

bug

cytomining/CytoDataFrame#31 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Speckles images issues within example notebook Open

bug

cytomining/CytoDataFrame#32 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add capability to read images from valid S3 paths Open

enhancement

cytomining/CytoDataFrame#34 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Enable CytoTable format specific capabilities Open

enhancement

cytomining/CytoDataFrame#40 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Update `mask` parameter to prefer outline images instead Open

cytomining/CytoDataFrame#48 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Optionally display multiple outline overlays Open

enhancement

cytomining/CytoDataFrame#60 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Override CytoDataFrame parameters when provided and data source is another CytoDataFrame Open

bug

cytomining/CytoDataFrame#62 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Address bounding box display issues from example notebook Open

bug

cytomining/CytoDataFrame#92 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add 3D / z-slice scroll bar for image display selection Open

cytomining/CytoDataFrame#96 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add images from various angles as distinct columns for 3D datasets Open

cytomining/CytoDataFrame#97 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Consider new label for "image adjustment" label Open

cytomining/CytoDataFrame#106 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Address ignored linting rules to help improve code quality Open

enhancement

cytomining/CytoDataFrame#118 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Fix text-based output of CytoDataFrame Open

cytomining/CytoDataFrame#121 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add ability to export record feature data with image arrays Open

cytomining/CytoDataFrame#133 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add image scale display option labels (indicating measurement within images) Open

cytomining/CytoDataFrame#138 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Confirm CDF works with Marimo notebooks Open

cytomining/CytoDataFrame#154 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Handle multi-channel images Open

cytomining/CytoDataFrame#155 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Enable boundingbox cols to have "metadata" in the field name Open

cytomining/CytoDataFrame#158 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Tie all bounding boxes to relevant images Open

cytomining/CytoDataFrame#163 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add vortex file input / output capabilities Open

cytomining/CytoDataFrame#176 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Enable the use of arbitrary filepaths or arrays for use in image rendering with CDF instantiation Open

cytomining/CytoDataFrame#184 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Adjust cytodataframe styling for use with Google Colab Open

cytomining/CytoDataFrame#193 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Ensure image adjustments work for OME-Arrow derived visualizations Open

cytomining/CytoDataFrame#194 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Provide DataFrame row filtering based on column min and max thresholds Open

cytomining/CytoDataFrame#196 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Provide graceful message when no data can be displayed Open

cytomining/CytoDataFrame#197 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Filter columns plots are hard to see with small values like z-scores Open

cytomining/CytoDataFrame#205 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Enable and/or document explicit CytoTable iceberg compatibility Open

cytomining/CytoDataFrame#207 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Fix broken pypi deploy Open

cytomining/CytoDataFrame#211 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add column categorization enhancements Open

cytomining/CytoDataFrame#230 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026

cytomining/CytoDataFrame

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