Volume electron microscopy of the cerebral microvasculature — precapillary sphincters, pericytes, astrocyte endfeet and the brain's waste-clearance pathway. Open tools and open data for identifying cells in large EM volumes.
build 2026-10-19 11:06
Søren Grubb is a neuroscientist with a background in neurovascular research and cardiac electrophysiology.
There is no laboratory behind this. No bench, no funding and no staff — “Grubb Lab” is what the site is called, not a place you could visit. It is a hobby, built in spare time on electron microscopy volumes that other people collected, imaged and released publicly.
Five studies with collaborators in Hobart, Bethesda and Copenhagen — precapillary sphincters, microglia at the vessel wall, primary cilia on mural cells, the leptomeningeal fibroblasts and the brain's waste-clearance route. The findings, the figures, and the coordinates they were read from. Research & collaborations →
Cell positions, segmentation and type predictions come from the MICrONS minnie65 mouse visual cortex dataset, released under CC-BY by the MICrONS Consortium (Nature 640, 435–447, 2025). Hand-verified identifications, traced vessel outlines and traced pia/white-matter surfaces are original work from this lab.
δJump uses the Allen Institute's V1 Deep Dive (V1DD) volume of mouse visual cortex, released
publicly as the v1dd_public CAVE datastack
(Allen Institute
Connectomics); viewing its segmentation requires a free CAVE account. Its cortical layer
model is not taken from a published atlas — it is fitted here from the depths of the dataset's
own layer-named neuron types, after correcting for the tilt of the imaged block.
The code — the pages, core/*.js, the build scripts, the Apps
Script backend and the Colab and Blender exports — is under the
MIT License. The writing and the figures on this site and
inside the tools are under
CC BY 4.0.
Two licences rather than one because Creative Commons
recommends against using its
licences for software.
Neither covers the datasets. Every volume is read from its publisher's own cloud
bucket and none is redistributed here, so each dataset's own terms apply — and a
number of them state no reuse licence at all. The terms for each one are shown on its page.
The libraries bundled in core/vendor/ are third-party code under their
own licences, included unmodified with their notices beside them.
What you submit stays yours. Identifications, corrections, organelle reports, tracings and forum posts are released by the people who made them under CC BY 4.0, so the community annotation database can be shared and cited; contributors keep the copyright in their own work and are credited by name or handle. This applies to submissions made from 17 October 2026 onwards. You can ask for your contributions to be removed at any time.
µJump offers an optional Google sign-in. If you sign in, we store your Google display name and email address together with your contribution activity — the cells you identify, IDs you propose, votes, favourites and timestamps — in a private Google Sheet. This is used to attribute contributions, power your personal statistics, and rank a public leaderboard, which shows a chosen display name (never your email). Sign-in is required only to submit or save; you can browse and explore without it. To have your data removed, email soren@grubb.dk.
| Dataset | Year | Publication | Tissue | Species | Resolution | Size | To scale |
|---|---|---|---|---|---|---|---|
| minnie65µJump | 2025 | MICrONS Consortium, Nature 640 | cortex, V1 L1–6 | mouse | 4 × 4 × 40 nm | 1700 × 1400 × 500 µm 1.2 × 10⁹ µm³ | |
| V1DDδJump | — | Allen Institute — no paper | cortex, V1 full depth | mouse | 9 × 9 × 45 nm | 1800 × 1100 × 800 µm 1.6 × 10⁹ µm³ | |
| pinky100πJump | 2022 | Dorkenwald et al., eLife 11 | cortex, V1 L2/3 | mouse | 4 × 4 × 40 nm | 360 × 215 × 87 µm 6.7 × 10⁶ µm³ | |
| lee16λJump | 2016 | Lee et al., Nature 532 | cortex, V1 L2/3 | mouse | 4 × 4 × 40 nm | 454 × 448 × 33 µm 6.7 × 10⁶ µm³ | |
| H01ηJump | 2024 | Shapson-Coe et al., Science 384 | cortex, temporal full depth | human | 8 × 8 × 33 nm | 3000 × 2000 × 170 µm 1.0 × 10⁹ µm³ | |
| cb2χJump | 2023 | Nguyen, Thomas et al., Nature 613 | cerebellar cortex, lobule V | mouse | 4 × 4 × 40 nm | 998 × 922 × 48 µm 4.4 × 10⁷ µm³ | |
| 3×Tg vCLEMβJump | 2023 | Han, Wei et al., bioRxiv — preprint | hippocampus, CA1 | mouse | 8 × 8 × 30 nm | 240 × 245 × 26 µm 1.5 × 10⁶ µm³ |
| Dataset | Year | Publication | Tissue | Species | Resolution | Size | To scale |
|---|---|---|---|---|---|---|---|
| Brain · 34 volumes | |||||||
| wk-ppc2 | 2020 | Karimi et al. | cortex L1-5 (PPC-2) | mouse | 11.24×11.24×30 nm | 291 × 622 × 397 µm 7.2 × 10⁷ µm³ | |
| wk-karimi-lpta | 2020 | Karimi et al. | cortex (LPtA) | mouse | 11.24×11.24×30 nm | 391 × 230 × 737 µm 6.6 × 10⁷ µm³ | |
| wk-morgan2020 | 2020 | Morgan et al. | thalamus (dLGN) | mouse | 4×4×30 nm | 444 × 510 × 274 µm 6.2 × 10⁷ µm³ | |
| wk-bock11 | 2011 | Bock et al. | cortex (V1) + leptomeninges | mouse | 4×4×40 nm | 541 × 373 × 49 µm 1.0 × 10⁷ µm³ | |
| wk-bloss18 | 2018 | Bloss et al. | hippocampus | mouse | 3.89×3.89×50 nm | 272 × 393 × 16 µm 1.7 × 10⁶ µm³ | |
| wk-karimi-s1 | 2020 | Karimi et al. | cortex (S1) | mouse | 11.24×11.24×28 nm | 101 × 67 × 219 µm 1.5 × 10⁶ µm³ | |
| wk-gour21-p7-l4 | 2021 | Gour et al. | cortex L4 (barrel, P7) | mouse | 11.24×11.24×30 nm | 77 × 111 × 161 µm 1.4 × 10⁶ µm³ | |
| wk-v2 | 2020 | Karimi et al. | cortex L2/3 (V2) | mouse | 12×12×30 nm | 77 × 98 × 154 µm 1.2 × 10⁶ µm³ | |
| wk-acc | 2020 | Karimi et al. | cortex L2 (ACC) | mouse | 12×12×30 nm | 77 × 146 × 99 µm 1.1 × 10⁶ µm³ | |
| wk-ppc | 2020 | Karimi et al. | cortex (PPC) | mouse | 12×12×30 nm | 78 × 98 × 146 µm 1.1 × 10⁶ µm³ | |
| wk-ex144-l23-s1 | 2022 | Loomba et al. | cortex L2/3 (S1) | mouse | 11.24×11.24×28 nm | 89 × 57 × 214 µm 1.1 × 10⁶ µm³ | |
| bd-wb23-mouse-v1-l4-p105 | 2023 | Wildenberg et al. | cortex L4 (V1, P105) | mouse | 6×6×40 nm | 126 × 139 × 38 µm 6.7 × 10⁵ µm³ | |
| bd-wb23-mouse-v1-l4-p14 | 2023 | Wildenberg et al. | cortex L4 (V1, P14) | mouse | 6×6×40 nm | 90 × 125 × 54 µm 6.0 × 10⁵ µm³ | |
| wk-ex145-l4-s1 | 2019 | Motta et al. | cortex L4 (S1) | mouse | 11.24×11.24×28 nm | 62 × 95 × 93 µm 5.4 × 10⁵ µm³ | |
| bd-wb23-mouse-v1-l4-p6 | 2023 | Wildenberg et al. | cortex L4 (V1, P6) | mouse | 6×6×40 nm | 126 × 137 × 19 µm 3.2 × 10⁵ µm³ | |
| bd-wb23-mouse-v1-l23-p105 | 2023 | Wildenberg et al. | cortex L2/3 (V1, P105) | mouse | 6×6×40 nm | 100 × 108 × 30 µm 3.2 × 10⁵ µm³ | |
| wk-kasthuri2011 | 2015 | Kasthuri et al. | cortex | mouse | 6×6×30 nm | 65 × 80 × 56 µm 2.9 × 10⁵ µm³ | |
| bd-wb23-mouse-v1-l23-p523 | 2023 | Wildenberg et al. | cortex L2/3 (V1, P523) | mouse | 6×6×40 nm | 96 × 112 × 22 µm 2.4 × 10⁵ µm³ | |
| jrc_mus-choroid-plexus-3 | 2021 | Xu et al. | choroid plexus | mouse | 8 nm iso | 60 × 60 × 60 µm 2.2 × 10⁵ µm³ | |
| bd-wb21-nac-dopamine-cocaine | 2021 | Wildenberg et al. et al. | nucleus accumbens (dopamine axons, cocaine) | mouse | 4×4×40 nm | 72 × 97 × 30 µm 2.1 × 10⁵ µm³ | |
| bd-wb23-mouse-v1-l4-p523 | 2023 | Wildenberg et al. | cortex L4 (V1, P523) | mouse | 6×6×40 nm | 83 × 95 × 23 µm 1.8 × 10⁵ µm³ | |
| wk-h5-l23-msem | 2022 | Loomba et al. | cortex L2/3 (STG), MultiSEM | human | 4×4×38 nm | 1409 × 1331 × 88 µm 1.6 × 10⁸ µm³ | |
| wk-h5-l16-msem | 2022 | Loomba et al. | cortex L1-6 (STG), MultiSEM | human | 4×4×37 nm | 1917 × 2553 × 30 µm 1.4 × 10⁸ µm³ | |
| wk-h5-l23-stg | 2022 | Loomba et al. | cortex L2/3 (STG) | human | 11.24×11.24×30 nm | 167 × 216 × 113 µm 4.1 × 10⁶ µm³ | |
| wk-h6-l23-ifg | 2022 | Loomba et al. | cortex L2/3 (IFG) | human | 11.24×11.24×30 nm | 170 × 216 × 79 µm 2.9 × 10⁶ µm³ | |
| wk-mk1-t2-stg | 2022 | Loomba et al. | cortex L2/3 (STG) | macaque | 11.24×11.24×30 nm | 179 × 228 × 108 µm 4.4 × 10⁶ µm³ | |
| wk-mk1-f6-l23 | 2022 | Loomba et al. | cortex L2/3 (S1) | macaque | 11.24×11.24×30 nm | 168 × 220 × 101 µm 3.7 × 10⁶ µm³ | |
| bd-wb23-primate-v1-l23-p75 | 2023 | Wildenberg et al. | cortex L2/3 (V1, P75) | macaque | 6×6×40 nm | 123 × 135 × 38 µm 6.3 × 10⁵ µm³ | |
| bd-wb23-primate-v1-l23-p7 | 2023 | Wildenberg et al. | cortex L2/3 (V1, P7) | macaque | 6×6×40 nm | 124 × 121 × 16 µm 2.4 × 10⁵ µm³ | |
| bd-wb23-primate-v1-l23-p3000 | 2023 | Wildenberg et al. | cortex L2/3 (V1, P3000) | macaque | 6×6×40 nm | 91 × 95 × 27 µm 2.3 × 10⁵ µm³ | |
| bd-wb23-primate-v1-l4-p3000 | 2023 | Wildenberg et al. | cortex L4 (V1, P3000) | macaque | 6×6×40 nm | 125 × 120 × 15 µm 2.2 × 10⁵ µm³ | |
| wk-denk2004 | 2004 | Denk et al. | cortex | rat | 10×10×50 nm | 20 × 18 × 98 µm 3.6 × 10⁴ µm³ | |
| wk-wanner16 | 2016 | Wanner et al. | olfactory bulb | zebrafish | 9×9×25 nm | 121 × 135 × 138 µm 2.2 × 10⁶ µm³ | |
| wk-j0256 | 2017 | Kornfeld et al. | HVC (song nucleus) | zebra finch | 11×11×29 nm | 166 × 166 × 77 µm 2.1 × 10⁶ µm³ | |
| Retina · 6 volumes | |||||||
| ew2-stroeh-retina | 2026 | Ströh et al. | retina (Eyewire II) | mouse | 16×16×40 nm | 1311 × 1311 × 83 µm 1.4 × 10⁸ µm³ | |
| wk-k0725 | 2016 | Ding et al. | retina (k0725) | mouse | 13.2×13.2×26 nm | 66 × 211 × 263 µm 3.7 × 10⁶ µm³ | |
| wk-e2006 | 2013 | Helmstaedter et al. | retina (e2006) | mouse | 16.5×16.5×25 nm | 135 × 122 × 86 µm 1.4 × 10⁶ µm³ | |
| wk-k0563 | 2011 | Briggman et al. | retina (k0563) | mouse | 12×12×25 nm | 55 × 66 × 144 µm 5.3 × 10⁵ µm³ | |
| bd-ish21-retina-opl-em2 | 2021 | Ishibashi et al. | retina, outer plexiform layer (EM2) | mouse | 4 nm iso | 27 × 18 × 5.4 µm 2.6 × 10³ µm³ | |
| bd-ish21-retina-opl-em1 | 2021 | Ishibashi et al. | retina, outer plexiform layer (EM1) | mouse | 4 nm iso | 25 × 16 × 4.5 µm 1.8 × 10³ µm³ | |
| Spinal cord · 1 volume | |||||||
| wk-zf-vertebra | 2021 | Guan et al. | spinal cord | zebrafish | 12×12×35 nm | 251 × 188 × 248 µm 1.2 × 10⁷ µm³ | |
| Peripheral nervous system · 3 volumes | |||||||
| jrc_mus-pacinian-corpuscle | 2021 | Xu et al. | Pacinian corpuscle | mouse | 6 nm iso | 58 × 63 × 291 µm 1.1 × 10⁶ µm³ | |
| wk-meissner-sham | 2022 | Gangadharan et al. | Meissner corpuscle (sham, SBEM) | mouse | 11.24×11.24×30 nm | 114 × 72 × 39 µm 3.2 × 10⁵ µm³ | |
| jrc_mus-meissner-corpuscle-1 | 2021 | Xu et al. | Meissner corpuscle | mouse | 6 nm iso | 37 × 46 × 58 µm 9.8 × 10⁴ µm³ | |
| Inner ear · 1 volume | |||||||
| wk-cochlea | 2021 | Hua et al. | cochlea | mouse | 11×11×40 nm | 188 × 101 × 100 µm 1.9 × 10⁶ µm³ | |
| Heart · 2 volumes | |||||||
| jrc_mus-heart-1 | 2021 | Xu et al. | heart | mouse | 8 nm iso | 163 × 152 × 136 µm 3.4 × 10⁶ µm³ | |
| jrc_zf-cardiac-1 | 2021 | Xu et al. | heart | zebrafish | 8 nm iso | 165 × 159 × 321 µm 8.4 × 10⁶ µm³ | |
| Kidney · 3 volumes | |||||||
| jrc_mus-kidney-2 | 2021 | Xu et al. | kidney (kidney-2) | mouse | 8 nm iso | 103 × 101 × 111 µm 1.2 × 10⁶ µm³ | |
| jrc_mus-kidney | 2021 | Xu et al. | kidney | mouse | 8 nm iso | 98 × 64 × 178 µm 1.1 × 10⁶ µm³ | |
| jrc_ut21-1413-003 | 2021 | Xu et al. | kidney (renal carcinoma) | human | 8 nm iso | 121 × 91 × 130 µm 1.4 × 10⁶ µm³ | |
| Liver · 3 volumes | |||||||
| jrc_mus-liver-zon-2 | 2021 | Xu et al. | liver (zonation, zon-2) | mouse | 8 nm iso | 210 × 156 × 427 µm 1.4 × 10⁷ µm³ | |
| jrc_mus-liver-zon-1 | 2021 | Xu et al. | liver (zonation, zon-1) | mouse | 8 nm iso | 189 × 172 × 397 µm 1.3 × 10⁷ µm³ | |
| jrc_mus-liver | 2021 | Xu et al. | liver | mouse | 8 nm iso | 102 × 102 × 71 µm 7.4 × 10⁵ µm³ | |
| Skeletal muscle · 1 volume | |||||||
| jrc_mus-skel-muscle-1 | 2021 | Xu et al. | skeletal muscle | mouse | 8 nm iso | 101 × 61 × 20 µm 1.3 × 10⁵ µm³ | |
| Pancreas · 2 volumes | |||||||
| jrc_mus-pancreas-4 | 2021 | Xu et al. | pancreas | mouse | 8 nm iso | 146 × 113 × 115 µm 1.9 × 10⁶ µm³ | |
| jrc_mus-pancreas-2 | 2021 | Xu et al. | pancreas (pancreas-2) | mouse | 4 nm iso | 20 × 20 × 30 µm 1.2 × 10⁴ µm³ | |
| Thymus · 1 volume | |||||||
| jrc_mus-thymus-1 | 2021 | Xu et al. | thymus | mouse | 8 nm iso | 147 × 116 × 116 µm 2.0 × 10⁶ µm³ | |
| Skin · 2 volumes | |||||||
| jrc_mus-skin-1 | 2021 | Xu et al. | skin | mouse | 8 nm iso | 138 × 114 × 158 µm 2.5 × 10⁶ µm³ | |
| jrc_mus-guard-hair-follicle | 2021 | Xu et al. | guard hair follicle | mouse | 6 nm iso | 88 × 96 × 78 µm 6.6 × 10⁵ µm³ | |
| Airway · 1 volume | |||||||
| jrc_hum-airway-14953vc | 2021 | Xu et al. | airway epithelium | human | 8 nm iso | 213 × 103 × 121 µm 2.6 × 10⁶ µm³ | |
| Lung · 1 volume | |||||||
| jrc_mus-lung-2a | 2021 | Xu et al. | lung | mouse | 8 nm iso | 121 × 62 × 62 µm 4.6 × 10⁵ µm³ | |
| Duodenum · 1 volume | |||||||
| jrc_mus-duodenum-1a | 2021 | Xu et al. | duodenum | mouse | 8 nm iso | 111 × 62 × 41 µm 2.8 × 10⁵ µm³ | |