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6876b91
add notebook using PENGUIN to preprocess IMC and IF
marta-seq Jan 25, 2026
1031b4a
add notebook that explores Cosmx agridgene vs reference. start with X…
marta-seq Jan 25, 2026
4a333ad
update notebook that explores agridgene vs reference. Xenium
marta-seq Jan 26, 2026
1e87b01
update notebook that explores agridgene vs reference. Xenium
marta-seq Jan 26, 2026
082a72b
update on quantitative xenium
marta-seq Feb 4, 2026
ac3d6ae
add quantitative validation for cell validation
marta-seq Feb 6, 2026
3fd7adb
add quantitative validation for cell validatio changesn
marta-seq Feb 7, 2026
e44e8af
add runtime analysis
marta-seq Feb 8, 2026
2835f10
WIP: current work before branch restructure
marta-seq Feb 8, 2026
63600c4
clean and improve runtime with clear subprocesses benchmarks
marta-seq Feb 8, 2026
e1ed564
fix on binsom logger
marta-seq Feb 8, 2026
2cafeef
refactor of quant analysis. fix cosmx and IF
marta-seq Feb 9, 2026
f9bdc49
update on validation code for Xeniuma nd CosMx
marta-seq Feb 10, 2026
4c01f3b
update notebook xenium quantitative
marta-seq Feb 12, 2026
63aded9
add function on validation
marta-seq Feb 12, 2026
144dc3d
fix the cell phenotyping overlap with gridgene masks
marta-seq Feb 13, 2026
656da38
add plot on Xenium part
marta-seq Feb 18, 2026
eca3435
fix plots runtime_performance and clean code
marta-seq Feb 23, 2026
4581012
include instalation guidelines
marta-seq Feb 23, 2026
88c888c
orthogonal validation cell segmentation
marta-seq Mar 11, 2026
cb5dcde
orthogonal validation cell segmentation imporvment
marta-seq Mar 14, 2026
85b628a
validation against manual masks. deletion of redundant notebooks
marta-seq Mar 14, 2026
cdfee02
remove tracked folders
marta-seq Mar 14, 2026
e552491
add new notebook on gd xenium validation
marta-seq Mar 14, 2026
0677448
add new notebook on gd xenium validation - small fixes
marta-seq Apr 6, 2026
a85010f
clean and improve images orthogonal ipynb
marta-seq Apr 11, 2026
65a69c2
clean and improve images orthogonal ipynb
marta-seq Apr 12, 2026
f60ed67
clean and improve images manual annotation ipynb
marta-seq Apr 12, 2026
b482bdb
remove figures from tracking, add to gitignore
marta-seq Apr 12, 2026
355ae3f
remove to_delete folder from tracking
marta-seq Apr 12, 2026
aedde91
remove benchmark_plots from tracking
marta-seq Apr 12, 2026
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10 changes: 10 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ regions of interest based on transcript density. It enables the identification o

## Table of Contents
- [Features](#features)
- [Installation](#Installation)
- [Documentation](#documentation)
- [Credits](#credits)
- [License](#license)
Expand All @@ -36,6 +37,15 @@ GRIDGENE contains the following Case Studies:
- Alternative masking strategies using KD-Trees and Self-Organizing Maps (SOM)

---
## Installation

GRIDGENE requires Python >= 3.10.
```bash
git clone https://github.com/deMirandaLab/GRIDGENE.git
cd GRIDGENE
pip install -e .
```
---

## Documentation

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