nuclei
Datasets
All datasets matching “nuclei”cross-channel-nuclei-from-cellmask
Cross-channel nuclei-from-cellmask dataset
3029 paired fields. images/ is the
cell-mask input channel, masks/ the matching instance-labelled nuclei ground truth (same stem =
same field). split_by_well.csv gives the train/test assignment; the split is by well, so no
well contributes to both sides - field-level splitting would leak.
Prepared with spaCR
(PyPI | conda-forge).
Used to train einarolafsson/cross-channel-nuclei-from-cellmask-cpsam.
Pan-Cancer-Nuclei-Seg
Pan-Cancer-Nuclei-Seg — Manual Subset
Gold-standard manual nucleus segmentation patches from the TCIA
Pan-Cancer-Nuclei-Seg resource (Hou et al., Scientific Data 2020): 1,356
manually segmented 256×256 H&E patches with per-nucleus instance masks,
spanning 14 TCGA cancer types.
Scope — please read. This repository contains only the manual subset,
not the full Pan-Cancer-Nuclei-Seg resource. The headline "~5 billion nuclei"
component (5,060 whole-slide images, ~666 GB of CSV… See the full description on the dataset page: https://huggingface.co/datasets/MedOtter/Pan-Cancer-Nuclei-Seg.pan-cancer-nuclei-seg
Nuclear Aging Morphometry Dataset: TCGA Bladder Cancer Nuclei Features for Longevity Research
Dataset Description
This dataset provides nuclear morphometric features extracted from TCGA bladder cancer histopathology slides, specifically designed for aging and longevity research. The dataset contains quantitative shape measurements of >1M individual nuclei across multiple fields of view, enabling machine learning approaches to study cellular aging, senescence biomarkers… See the full description on the dataset page: https://huggingface.co/datasets/longevity-db/pan-cancer-nuclei-seg.ernest-nuclei-templates-v3
Ernest Nuclei Templates Dataset v3
A comprehensive dataset for training models to generate Nuclei security scanning templates from vulnerability descriptions.
Dataset Description
This dataset contains 11,590 training examples for generating Nuclei YAML templates in JSON IR (Intermediate Representation) format from structured vulnerability specifications.
Format
Each training example consists of:
id: Unique identifier (CVE ID, CWE ID, or template name)
prompt:… See the full description on the dataset page: https://huggingface.co/datasets/OzLabs/ernest-nuclei-templates-v3.ernest-nuclei-templates-v1-instruct
Ernest Nuclei Templates Dataset v1 (Instruction Format)
This is a restructured version of the Ernest Nuclei Templates dataset optimized for instruction tuning.
Format
Each example has this structure:
{
"instruction": "Generate a Nuclei template for CVE-2024-1234",
"input": "Title: XSS in Product\nSummary: Description...\nSeverity: high",
"output": "id: cve-2024-1234\n\ninfo:\n name: ...\n\nhttp:\n - method: GET\n ...",
"category": "cve",
"severity": "high"… See the full description on the dataset page: https://huggingface.co/datasets/guychuk/ernest-nuclei-templates-v1-instruct.synthetic-nuclei-vessel
Dataset generation and attribution
These synthetic nuclei–vessel datasets were generated with the
TDBase synthetic-data simulator,
using the upstream TDBase commit
5058e2f540438a497cd0592b9044e0bcbd745cbb.
Generation used TDBase nucleus and vessel prototype meshes, and the
following configuration: 750 vessels, 200/400/600/800 nuclei per
vessel, radius 30, Hausdorff preprocessing, and intersection-enabled
placement.
TDBase is distributed under GPL-3.0. This dataset contains… See the full description on the dataset page: https://huggingface.co/datasets/HPI-Pierce/synthetic-nuclei-vessel.