cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/sde-wtr-ngr
title: Myrica gale L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdf-96z-wnd
title: Anthoxanthum nitens (Weber) Y.Schouten & Veldkamp

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdf-dyl-6jt
title: Trifolium arvense L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdf-gtz-szs
title: Chelidonium majus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdf-9a2-h7z
title: Corallorhiza trifida Châtel.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdf-k1e-w58
title: Rumex maritimus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdg-1wg-xsz
title: Rumex L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdg-2am-2l1
title: Festuca ovina L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdg-7xa-jj7
title: Equisetum pratense Ehrh.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdg-dqh-ch5
title: Butomus umbellatus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdg-gzs-yay
title: Trifolium spadiceum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdf-z4d-6kv
title: Trollius europaeus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdg-j0r-lva
title: Agrostis gigantea Roth

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdg-r2q-jz3
title: Lathyrus linifolius (Reichard) Bässler

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdg-ycb-bgc
title: Triglochin maritima L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdh-1yb-z0b
title: Carex limosa L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdh-2my-p6l
title: Plantago lanceolata L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdh-a93-phj
title: Phalaris canariensis L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdh-dbs-q7n
title: Sagittaria × lunata C.D.Preston & Uotila

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdh-j2l-0h3
title: Carex disperma Dewey

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdh-mm2-lqq
title: Salix caprea × repens subsp. repens

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdh-spa-z8w
title: Filipendula vulgaris Moench

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdh-tc8-a2t
title: Chenopodium pratericola Rydb.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdh-wgy-1f3
title: Atocion rupestre (L.) Oxelman

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdh-xqn-4th
title: Najas marina L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdh-9hy-nrv
title: Betula pendula Roth

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdj-443-gfs
title: Eriophorum angustifolium Honck.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdh-a45-36p
title: Plantae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.5281/zenodo.18011833
title: MERFISH data from the murine hypothalamus in health and under induced sickness states

description: In natural environments, animals encounter diverse pathogens that engage specific peripheral host defense programs and elicit sickness behavior – a set of stereotyped physiological and behavioral changes thought to promote host fitness. So far, most studies have relied on one or few mouse models of infection, limiting insights into pathogen-specific neuroimmune interactions that generate sickness.

We hypothesized that different pathogens may elicit distinct sickness states and engage various brain circuits. Using different models of infection and inflammation representing bacterial, viral, allergic, parasitic and colitis conditions, we assessed sickness across scales: organismal – behavior and physiology; cellular – brain-wide neural activity; and molecular – single-cell in situ transcriptomics in the hypothalamus, associated with social and homeostatic functions affected during sickness. Remarkably, immune challenges each elicited unique repertoires of changes across all scales. Our findings reveal specific pathogen-specific sickness states encoded by the brain across scales, thereby broadening our understanding of how infections make us sick.

This repository contains MERFISH-related data associated with these studies.   

Namely it contains the merfish_adata.h5ad file. 

This file was created from the scanpy package and can be loaded with tools from that package.  It contains the following items:

* X: The matrix of expression for all cells and all genes. This matrix was divided by total counts per cell then log1p-transformed.* obs: A dataframe with the following properties for all cells  The index of each row in this data frame is a unique name for each cell  * batch: A unique name for each MERFISH dataset  * x: The centroid of that cell in x, in microns  * y: The centroid of that cell in y, in microns  * z: The average position of that cell in z-stacks, in microns  * cellType: The cell type label associated with that cell  * condition: The treatment condition for the mouse in which the cell was imaged  * section: An index for the section in which the cell was imaged  * ignoreCell: A flag that indicates that the cell was not included in subsequent analysis
DOI: 10.5281/zenodo.18011834
title: MERFISH data from the murine hypothalamus in health and under induced sickness states

description: In natural environments, animals encounter diverse pathogens that engage specific peripheral host defense programs and elicit sickness behavior – a set of stereotyped physiological and behavioral changes thought to promote host fitness. So far, most studies have relied on one or few mouse models of infection, limiting insights into pathogen-specific neuroimmune interactions that generate sickness.

We hypothesized that different pathogens may elicit distinct sickness states and engage various brain circuits. Using different models of infection and inflammation representing bacterial, viral, allergic, parasitic and colitis conditions, we assessed sickness across scales: organismal – behavior and physiology; cellular – brain-wide neural activity; and molecular – single-cell in situ transcriptomics in the hypothalamus, associated with social and homeostatic functions affected during sickness. Remarkably, immune challenges each elicited unique repertoires of changes across all scales. Our findings reveal specific pathogen-specific sickness states encoded by the brain across scales, thereby broadening our understanding of how infections make us sick.

This repository contains MERFISH-related data associated with these studies.   

Namely it contains the merfish_adata.h5ad file. 

This file was created from the scanpy package and can be loaded with tools from that package.  It contains the following items:

* X: The matrix of expression for all cells and all genes. This matrix was divided by total counts per cell then log1p-transformed.* obs: A dataframe with the following properties for all cells  The index of each row in this data frame is a unique name for each cell  * batch: A unique name for each MERFISH dataset  * x: The centroid of that cell in x, in microns  * y: The centroid of that cell in y, in microns  * z: The average position of that cell in z-stacks, in microns  * cellType: The cell type label associated with that cell  * condition: The treatment condition for the mouse in which the cell was imaged  * section: An index for the section in which the cell was imaged  * ignoreCell: A flag that indicates that the cell was not included in subsequent analysis
DOI: 10.3535/sdj-bjz-3rc
title: Carex digitata L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdj-f5d-klv
title: Sparganium natans L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdj-hxw-ah2
title: Fragaria vesca L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdj-k80-0p6
title: Actaea spicata L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdj-klj-w1b
title: Plantae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdj-ndc-lln
title: Rumex maritimus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdj-tny-sxl
title: Rubus idaeus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdj-vev-pr8
title: Potamogeton pusillus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdj-wgv-8lr
title: Carex nigra subsp. juncea (Fr.) Soó

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdj-ymd-0q9
title: Rumex pseudonatronatus (Borbás) Borbás ex Murb.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdk-0bm-xz3
title: Rhodiola rosea L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdk-89k-nad
title: Danthonia decumbens (L.) DC.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdk-hgb-fmd
title: Lathyrus pratensis L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdk-jqz-h17
title: Sisymbrium officinale (L.) Scop.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdk-lgc-8rc
title: Epipactis helleborine (L.) Crantz

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdk-m21-k0a
title: Carex atrata L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdk-rcs-ew4
title: Selaginoides spinulosa (A. Braun ex Döll) Li Bing Zhang & X. M. Zhou

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdk-rsm-j93
title: Vicia hirsuta (L.) Gray

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdk-sae-ge6
title: Schoenus ferrugineus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdk-tlb-2jh
title: Chenopodium L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdk-vxw-e0c
title: Zannichellia palustris subsp. major (Hartm.) Ooststr. & Reichg.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdk-xck-kkp
title: Rumex crispus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdl-97v-6c7
title: Sisymbrium loeselii L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdl-qt4-2fq
title: Drosera intermedia Hayne

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdl-t4g-svn
title: Equisetum pratense Ehrh.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdl-yw5-1te
title: Rubus chamaemorus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdm-27w-86v
title: Crassula aquatica (L.) Schönland

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdm-tdy-2dw
title: Salix rosmarinifolia subsp. rosmarinifolia

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdm-zn8-fxh
title: Equisetum palustre L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdl-px2-74c
title: Salix cinerea L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdm-nwv-0gv
title: Potentilla L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdn-1jz-5g9
title: Sparganium natans L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdn-2ry-3wt
title: Plantae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdn-k4v-2j6
title: Ribes L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdn-kny-gcy
title: Malus baccata (L.) Borkh.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdn-l6c-cl6
title: Betula pubescens Ehrh.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdn-t64-kat
title: Rabelera holostea (L.) M. T. Sharples & E. A. Tripp

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdn-x6r-8wz
title: Potentilla crantzii (Crantz) Beck ex Fritsch

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdn-yhw-gng
title: Najas marina L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdn-z8r-5yg
title: Geranium bohemicum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdn-zjl-r2q
title: Carex nigra subsp. juncea (Fr.) Soó

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdn-ztv-yv5
title: Carex loliacea L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdp-09y-wj9
title: Spinulum annotinum (L.) A. Haines

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdp-74a-thd
title: Dichodon cerastoides (L.) Rchb.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdp-7tt-j7d
title: Scheuchzeria palustris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdp-b5y-cq1
title: Carex arenaria L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdp-bdl-q0a
title: Trichophorum alpinum (L.) Pers.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdn-9en-x1z
title: Luzula multiflora (Ehrh.) Lej.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdp-ghw-kq4
title: Lathyrus vernus (L.) Bernh.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdp-v7y-yqr
title: Calamagrostis purpurea (Trin.) Trin.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdp-whk-q30
title: Carex disticha Huds.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdp-zr6-skq
title: Chenopodium suecicum Murr

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdq-4xk-zh6
title: Cystopteris dickieana R. Sim

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdq-62s-kej
title: Luzula pallescens Sw.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdq-ar5-s4m
title: Carex aquatilis Wahlenb.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdq-dyx-sqs
title: Dianthus arenarius L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdq-h3a-ktq
title: Equisetum sylvaticum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdq-0dh-gb1
title: Chenopodium L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdq-k5q-shz
title: Lathyrus palustris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdq-a97-m82
title: Trifolium pratense L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdq-fhz-bfj
title: Luzula pallescens Sw.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdq-hsz-nab
title: Neottia cordata (L.) Rich.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdq-sbb-k0n
title: Spergula morisonii Boreau

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdq-tba-6lw
title: Carex acuta L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdr-361-361
title: Juncus × inundatus Drejer

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdr-3q3-crd
title: Rumex acetosa L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdr-3zx-t8w
title: Brassica rapa subsp. sylvestris (L.) Janch.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdr-5l4-2np
title: Diphasiastrum alpinum (L.) Holub

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdr-693-4xq
title: Alchemilla acutiloba Opiz

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdr-ckg-st7
title: Alchemilla filicaulis Buser

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdr-qe9-06h
title: Alopecurus arundinaceus Poir.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdr-t1g-d2c
title: Carex brunnescens (Pers.) Poir.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdr-tp6-nmf
title: Sinapis alba L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdr-v8e-t09
title: Deschampsia cespitosa subsp. bottnica

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdr-zyh-c2j
title: Sinapis alba L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sds-a41-che
title: Erodium cicutarium (L.) L'Hér.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sds-bnh-gcr
title: Betula nana × pendula × pubescens

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sds-m13-5n4
title: Poa pratensis L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sds-pxe-msz
title: Urtica dioica var. subsp. dioica var. dioica

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sds-rm4-3nv
title: Plantae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sds-tb9-l48
title: Fragaria viridis subsp. viridis

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sds-w1g-tff
title: Trifolium resupinatum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdt-59q-ql7
title: Ranunculus flammula subsp. flammula

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdt-7th-d8l
title: Sorbus aucuparia subsp. aucuparia

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdt-80g-jrr
title: Plantae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdt-9q1-k45
title: Woodsia ilvensis (L.) R. Br.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdt-9r1-nc2
title: Micranthes foliolosa (R. Br.) Gornall

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdt-h9t-824
title: Lolium perenne L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdt-m9z-00q
title: Pseudathyrium alpestre (Hoppe) Newman

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdt-2k6-11y
title: Salix rosmarinifolia subsp. rosmarinifolia

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdt-w20-2kc
title: Actaea spicata L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdt-x5e-jpm
title: Corylus avellana L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sdv-7ek-55g
title: Carex vesicaria L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.