Datasets:

MICS-Lab
/

novae

name stringlengths 9 67	n_cells int64 0 1.36M	n_spots int64 0 617k	n_genes int64 0 33.5k	n_proteins int64 0 63	technology stringclasses 5 values	tissue stringclasses 18 values	species stringclasses 3 values
Xenium_V1_Human_Colon_Cancer_P1_CRC_Add_on_FFPE_outs	307,762	0	422	0	xenium	colon	human
Xenium_V1_Human_Colon_Cancer_P2_CRC_Add_on_FFPE_outs	340,837	0	422	0	xenium	colon	human
HumanBreastCancerPatient1_region_0	713,121	0	500	0	merscope	breast	human
Xenium_V1_FFPE_Human_Breast_IDC_With_Addon_outs	576,963	0	380	0	xenium	breast	human
Xenium_V1_FFPE_TgCRND8_2_5_months_outs	53,913	0	346	0	xenium	brain	mouse
Xenium_V1_FFPE_TgCRND8_5_7_months_outs	58,682	0	347	0	xenium	brain	mouse
Xenium_V1_FFPE_TgCRND8_17_9_months_outs	62,268	0	347	0	xenium	brain	mouse
Xenium_V1_FFPE_wildtype_5_7_months_outs	58,685	0	347	0	xenium	brain	mouse
Xenium_V1_FFPE_wildtype_2_5_months_outs	58,231	0	347	0	xenium	brain	mouse
Xenium_V1_FFPE_wildtype_13_4_months_outs	59,935	0	347	0	xenium	brain	mouse
slide_0_0	282,694	0	200	0	null	v2	toy
slide_0_1	282,693	0	200	0	null	v2	toy
slide_0_2	282,692	0	200	0	null	v2	toy
slide_0_3	282,691	0	200	0	null	v2	toy
slide_0_4	282,690	0	200	0	null	v2	toy
10H064210813H0208914_down	140,139	0	0	63	cosmx	head_and_neck	human
10H064210813H0208914_up	112,155	0	0	63	cosmx	head_and_neck	human
14H007030716H0216858_down	98,220	0	0	63	cosmx	head_and_neck	human
14H007030716H0216858_up	126,341	0	0	63	cosmx	head_and_neck	human
13H079750314H0227010_down	140,368	0	0	63	cosmx	head_and_neck	human
14H042050615H0377937_down	50,300	0	0	63	cosmx	head_and_neck	human
13H079750314H0227010_up	191,141	0	0	63	cosmx	head_and_neck	human
14H042050615H0377937_up	64,347	0	0	63	cosmx	head_and_neck	human
Visium_HD_Human_Lung_Cancer_Fixed_Frozen	0	617,107	18,085	0	visium_hd	lung	human
DLPFC_151675	0	3,592	33,538	0	visium	brain	human
DLPFC_151673	0	3,639	33,538	0	visium	brain	human
DLPFC_151674	0	3,673	33,538	0	visium	brain	human
Xenium_V1_mouse_pup_outs	1,355,849	0	379	0	xenium	whole_mouse	mouse
Xenium_V1_mFemur_formic_acid_24hrdecal_section_outs	253,560	0	477	0	xenium	femur	mouse
Xenium_Preview_Human_Non_diseased_Lung_With_Add_on_FFPE_outs	295,883	0	392	0	xenium	lung	human
Xenium_V1_humanLung_Cancer_FFPE_outs	162,254	0	377	0	xenium	lung	human
Xenium_V1_Human_Ovarian_Cancer_Addon_FFPE_outs	247,636	0	480	0	xenium	ovarian	human
Xenium_V1_Human_Lung_Cancer_Addon_FFPE_outs	161,000	0	480	0	xenium	lung	human
Xenium_V1_Human_Ductal_Adenocarcinoma_FFPE_outs	235,099	0	380	0	xenium	pancreas	human
Xenium_V1_FFPE_Human_Breast_ILC_With_Addon_outs	365,604	0	379	0	xenium	breast	human
Xenium_V1_mFemur_EDTA_3daydecal_section_outs	348,141	0	476	0	xenium	femur	mouse
HumanUterineCancerPatient2-ROCostain_region_0	758,506	0	500	0	merscope	uterine	human
Xeniumranger_V1_hSkin_Melanoma_Add_on_FFPE_outs	87,499	0	382	0	xenium	skin	human
Xenium_V1_hColon_Non_diseased_Add_on_FFPE_outs	275,822	0	425	0	xenium	colon	human
Xenium_V1_hSkin_nondiseased_section_1_FFPE_outs	68,476	0	376	0	xenium	skin	human
HumanOvarianCancerPatient2Slice2_region_0	71,381	0	500	0	merscope	ovarian	human
HumanOvarianCancerPatient1_region_0	358,485	0	500	0	merscope	ovarian	human
Xenium_V1_Human_Colon_Cancer_P5_CRC_Add_on_FFPE_outs	275,998	0	422	0	xenium	colon	human
Xenium_V1_FFPE_Human_Brain_Healthy_With_Addon_outs	24,406	0	313	0	xenium	brain	human
Xenium_Preview_Human_Lung_Cancer_With_Add_on_2_FFPE_outs	531,165	0	392	0	xenium	lung	human
HumanLungCancerPatient2_region_0	836,739	0	500	0	merscope	lung	human
HumanLiverCancerPatient1_region_0	568,355	0	500	0	merscope	liver	human
HumanLiverCancerPatient2_region_0	598,141	0	500	0	merscope	liver	human
Xenium_V1_hPancreas_Cancer_Add_on_FFPE_outs	190,965	0	474	0	xenium	pancreas	human
HumanMelanomaPatient2_region_0	207,869	0	500	0	merscope	skin	human
Xenium_V1_FFPE_Human_Breast_IDC_outs	574,852	0	280	0	xenium	breast	human
HumanUterineCancerPatient2-RACostain_region_0	741,749	0	500	0	merscope	uterine	human
Xenium_V1_hSkin_Melanoma_Base_FFPE_outs	106,980	0	282	0	xenium	skin	human
Xenium_V1_hLung_cancer_section_outs	150,365	0	377	0	xenium	lung	human
Xenium_V1_hBoneMarrow_acute_lymphoid_leukemia_section_outs	225,906	0	477	0	xenium	bone_marrow	human
Xenium_V1_human_Pancreas_FFPE_outs	140,702	0	377	0	xenium	pancreas	human
Xenium_V1_hLiver_nondiseased_section_FFPE_outs	239,271	0	377	0	xenium	liver	human
cosmx_normal_liver	340,706	0	1,197	0	cosmx	liver	human
Xenium_V1_FFPE_Human_Breast_IDC_Big_2_outs	885,523	0	280	0	xenium	breast	human
Xenium_V1_FF_Mouse_Brain_MultiSection_2_outs	154,654	0	248	0	xenium	brain	mouse
HumanMelanomaPatient1_region_0	468,138	0	500	0	merscope	skin	human
HumanProstateCancerPatient2_region_0	993,825	0	500	0	merscope	prostate	human
Xenium_V1_hLiver_cancer_section_FFPE_outs	162,628	0	473	0	xenium	liver	human
Xenium_V1_mFemur_EDTA_PFA_3daydecal_section_outs	247,876	0	474	0	xenium	femur	mouse
HumanUterineCancerPatient1_region_0	843,285	0	500	0	merscope	uterine	human
Xenium_V1_FF_Mouse_Brain_MultiSection_3_outs	158,047	0	248	0	xenium	brain	mouse
Xenium_V1_hColon_Cancer_Add_on_FFPE_outs	587,115	0	425	0	xenium	colon	human
Xenium_Prime_Human_Lymph_Node_Reactive_FFPE_outs	708,983	0	4,622	0	xenium	lymph_node	human
Xenium_V1_hColon_Non_diseased_Base_FFPE_outs	270,984	0	325	0	xenium	colon	human
Xenium_V1_hKidney_nondiseased_section_outs	97,560	0	377	0	xenium	kidney	human
Xenium_V1_Human_Brain_GBM_FFPE_outs	816,769	0	480	0	xenium	brain	human
HumanProstateCancerPatient1_region_0	721,668	0	500	0	merscope	prostate	human
Xenium_V1_FFPE_Human_Breast_ILC_outs	356,746	0	280	0	xenium	breast	human
HumanLungCancerPatient1_region_0	353,762	0	500	0	merscope	lung	human
Xenium_V1_Human_Colorectal_Cancer_Addon_FFPE_outs	388,175	0	480	0	xenium	colon	human
Xenium_Prime_Human_Skin_FFPE_outs	112,551	0	4,705	0	xenium	skin	human
Xenium_V1_FFPE_Human_Brain_Glioblastoma_With_Addon_outs	40,887	0	318	0	xenium	brain	human
HumanOvarianCancerPatient2Slice1_region_0	254,347	0	500	0	merscope	ovarian	human
cosmx_pancreas	48,944	0	21,569	0	cosmx	pancreas	human
Xenium_Prime_Mouse_Brain_Coronal_FF_outs	63,173	0	4,593	0	xenium	brain	mouse
Xenium_V1_hColon_Cancer_Base_FFPE_outs	647,524	0	325	0	xenium	colon	human
cosmx_cancer_liver	463,972	0	1,197	0	cosmx	liver	human
HumanColonCancerPatient2_region_0	817,588	0	500	0	merscope	colon	human
Xenium_V1_hKidney_cancer_section_outs	56,510	0	377	0	xenium	kidney	human
Xenium_V1_hLymphNode_nondiseased_section_outs	377,985	0	377	0	xenium	lymph_node	human
Xenium_V1_hTonsil_follicular_lymphoid_hyperplasia_section_FFPE_outs	864,388	0	377	0	xenium	tonsil	human
Xenium_V1_mouse_Colon_FF_outs	219,797	0	378	0	xenium	colon	mouse
Xenium_V1_FF_Mouse_Brain_MultiSection_1_outs	162,033	0	248	0	xenium	brain	mouse
Xenium_V1_FFPE_Human_Brain_Alzheimers_With_Addon_outs	44,955	0	352	0	xenium	brain	human
Xenium_Prime_Human_Prostate_FFPE_outs	193,000	0	5,002	0	xenium	prostate	human
Xenium_V1_hTonsil_reactive_follicular_hyperplasia_section_FFPE_outs	1,349,620	0	377	0	xenium	tonsil	human
HumanOvarianCancerPatient2Slice3_region_0	212,425	0	500	0	merscope	ovarian	human
Xenium_V1_hPancreas_nondiseased_section_outs	103,901	0	377	0	xenium	pancreas	human
HumanColonCancerPatient1_region_0	677,451	0	500	0	merscope	colon	human
Xenium_V1_FFPE_Human_Breast_IDC_Big_1_outs	892,966	0	280	0	xenium	breast	human

Description

Full novae dataset, including:

All the spatial transcriptomics samples used to train Novae
Protein samples used in the article
Some Visium and Visium HD samples
Synthetic data samples

You can download this dataset from the API, see novae.load_dataset

See here the list of available models trained on this dataset.

Note that Novae was trained on the image-based spatial transcriptomics samples. This means that it was not trained on the Visium/VisiumHD samples and the spatial proteomics samples.

Cite us

Our article is published in Nature Methods. You can cite Novae as below:

Blampey, Q., Benkirane, H., Bercovici, N. et al. Novae: a graph-based foundation model for spatial transcriptomics data.
Nat Methods (2025). https://doi.org/10.1038/s41592-025-02899-6

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Models trained or fine-tuned on MICS-Lab/novae