diff --git a/packages/openneuro-app/src/scripts/dataset/mutations/create-mosaic.jsx b/packages/openneuro-app/src/scripts/dataset/mutations/create-mosaic.jsx
new file mode 100644
index 000000000..2fe1a1686
--- /dev/null
+++ b/packages/openneuro-app/src/scripts/dataset/mutations/create-mosaic.jsx
@@ -0,0 +1,67 @@
+import React from "react"
+import { gql, useMutation } from "@apollo/client"
+import PropTypes from "prop-types"
+import { Button } from "../../components/button/Button"
+import styled from "@emotion/styled"
+
+const ButtonRow = styled.div`
+ display: grid;
+ grid-template-columns: auto minmax(0, 1fr);
+ grid-gap: 1.3em;
+ place-items: start;
+`
+
+const SuccessMessage = styled.p({
+ color: "rgb(92, 184, 92)",
+})
+const InProgressMessage = styled.p({
+ color: "orange",
+})
+const ErrorMessage = styled.p({
+ color: "red",
+})
+
+const CREATE_MOSAIC = gql`
+ mutation createMosaic($datasetId: ID!, $ref: String!) {
+ createMosaic(datasetId: $datasetId, ref: $ref)
+ }
+`
+
+const CreateMosaic = ({ datasetId, revision }) => {
+ const [mosaicMutation, { data, loading, error }] = useMutation(
+ CREATE_MOSAIC,
+ )
+ const success = data && data.createMosaic
+ return (
+
+ {loading && (
+ Mosaic creation is starting.
+ )}
+ {error && An error has occurred.}
+ {success && Mosaic creation has begun.}
+
+
+
+ )
+}
+
+CreateMosaic.propTypes = {
+ datasetId: PropTypes.string,
+ revision: PropTypes.string,
+}
+
+export default CreateMosaic
diff --git a/packages/openneuro-app/src/scripts/dataset/routes/admin-datalad.jsx b/packages/openneuro-app/src/scripts/dataset/routes/admin-datalad.jsx
index 81e6620fa..dd817a8fc 100644
--- a/packages/openneuro-app/src/scripts/dataset/routes/admin-datalad.jsx
+++ b/packages/openneuro-app/src/scripts/dataset/routes/admin-datalad.jsx
@@ -4,6 +4,7 @@ import DatasetHistory from "../fragments/dataset-history.jsx"
import CacheClear from "../mutations/cache-clear.jsx"
import { HoldDeletion } from "../mutations/hold-deletion"
import AdminExports from "../mutations/admin-exports"
+import CreateMosaic from "../mutations/create-mosaic"
import { DatasetPageBorder } from "./styles/dataset-page-border"
import { HeaderRow3, HeaderRow4 } from "./styles/header-row"
import { DatasetEvents } from "../mutations/dataset-events"
@@ -38,6 +39,15 @@ const AdminDataset = ({ dataset }) => (
+ Create Mosaic PDF
+
+ Create a pdf containing a single slice of every anatomical image. Useful
+ for quickly finding non-defaced images.
+
+
+
+
+
Draft Head
{dataset.draft.head}
diff --git a/packages/openneuro-server/src/graphql/resolvers/mosaic.ts b/packages/openneuro-server/src/graphql/resolvers/mosaic.ts
new file mode 100644
index 000000000..578cc294f
--- /dev/null
+++ b/packages/openneuro-server/src/graphql/resolvers/mosaic.ts
@@ -0,0 +1,87 @@
+import config from "../../config"
+import { generateDataladCookie } from "../../libs/authentication/jwt"
+import { getDatasetWorker } from "../../libs/datalad-service"
+import Mosaic from "../../models/mosaic"
+import { checkDatasetWrite } from "../permissions"
+import type { GraphQLContext } from "../builder"
+
+export const mosaic = (dataset, _, _context: GraphQLContext) =>
+ Mosaic.findOne({
+ id: dataset.revision,
+ datasetId: dataset.id,
+ })
+ .exec()
+ .then(Boolean)
+
+/**
+ * Snapshot mosaic resolver
+ */
+export const snapshotMosaic = async (snapshot, _, context: GraphQLContext) => {
+ const dataset = {
+ id: snapshot.id.split(":")[0],
+ revision: snapshot.hexsha,
+ }
+ return mosaic(dataset, _, context)
+}
+
+/**
+ * Save mosaic data returned by the datalad service
+ *
+ * Returns only a boolean if successful or not
+ */
+export const updateMosaic = (obj, args) => {
+ return Mosaic.updateOne(
+ {
+ id: args.mosaic.id,
+ datasetId: args.mosaic.datasetId,
+ },
+ args.mosaic,
+ {
+ upsert: true,
+ },
+ )
+ .exec()
+ .then(() => true)
+}
+
+export const mosaicUrl = (datasetId, ref) => {
+ return `http://${
+ getDatasetWorker(
+ datasetId,
+ )
+ }/datasets/${datasetId}/mosaic/${ref}`
+}
+
+/**
+ * Request mosaic creation for a given commit
+ * @param {object} obj Parent resolver
+ * @param {object} args
+ * @param {string} args.datasetId Dataset accession number
+ * @param {string} args.ref Git hexsha
+ */
+export const createMosaic = async (
+ obj,
+ { datasetId, ref },
+ { user, userInfo }: Pick,
+) => {
+ await checkDatasetWrite(datasetId, user, userInfo)
+ try {
+ const response = await fetch(mosaicUrl(datasetId, ref), {
+ method: "POST",
+ body: JSON.stringify({}),
+ headers: {
+ cookie: generateDataladCookie(config)(userInfo),
+ },
+ })
+ if (response.status === 200) {
+ return true
+ } else {
+ return false
+ }
+ } catch (err) {
+ // Backend unavailable or lock failed
+ if (err) {
+ return false
+ }
+ }
+}
diff --git a/packages/openneuro-server/src/graphql/resolvers/mutation.ts b/packages/openneuro-server/src/graphql/resolvers/mutation.ts
index 305191959..63e84c67b 100644
--- a/packages/openneuro-server/src/graphql/resolvers/mutation.ts
+++ b/packages/openneuro-server/src/graphql/resolvers/mutation.ts
@@ -19,6 +19,7 @@ import {
import { removeUser, setAdmin, setBlocked, updateUser } from "./user.js"
import { updateSummary } from "./summary"
import { revalidate, updateValidation } from "./validation.js"
+import { createMosaic, updateMosaic } from "./mosaic.js"
import {
removePermissions,
updateOrcidPermissions,
@@ -70,6 +71,7 @@ const Mutation = {
deleteSnapshot,
updateSummary,
updateValidation,
+ updateMosaic,
updatePublic,
updatePermissions,
updateOrcidPermissions,
@@ -93,6 +95,7 @@ const Mutation = {
finishUpload,
cacheClear,
revalidate,
+ createMosaic,
fsckDataset,
holdDeletion,
prepareRepoAccess,
diff --git a/packages/openneuro-server/src/graphql/resolvers/snapshots.ts b/packages/openneuro-server/src/graphql/resolvers/snapshots.ts
index de2102943..bbd570019 100644
--- a/packages/openneuro-server/src/graphql/resolvers/snapshots.ts
+++ b/packages/openneuro-server/src/graphql/resolvers/snapshots.ts
@@ -16,6 +16,7 @@ import { getRedis } from "../../libs/redis"
import CacheItem, { CacheType } from "../../cache/item"
import { normalizeDOI } from "../../libs/doi/normalize"
import { snapshotValidation } from "./validation"
+import { snapshotMosaic } from "./mosaic"
import { advancedDatasetSearchConnection } from "./dataset-search"
import { contributors } from "../../datalad/contributors"
import { getDraftInfo } from "../../datalad/draft"
@@ -334,6 +335,7 @@ const Snapshot = {
issues: (snapshot) => snapshotIssues(snapshot),
issuesStatus: (snapshot) => issuesSnapshotStatus(snapshot),
validation: snapshotValidation,
+ mosaic: snapshotMosaic,
contributors: (snapshot) => {
const datasetId = snapshot.datasetId
return contributors({
diff --git a/packages/openneuro-server/src/graphql/schema/inputs.ts b/packages/openneuro-server/src/graphql/schema/inputs.ts
index 7edb7f75d..af8eb1567 100644
--- a/packages/openneuro-server/src/graphql/schema/inputs.ts
+++ b/packages/openneuro-server/src/graphql/schema/inputs.ts
@@ -140,6 +140,13 @@ export const ValidatorInput = builder.inputType("ValidatorInput", {
}),
})
+export const MosaicInput = builder.inputType("MosaicInput", {
+ fields: (t) => ({
+ id: t.id({ required: true }),
+ datasetId: t.id({ required: true }),
+ }),
+})
+
export const MetadataInput = builder.inputType("MetadataInput", {
fields: (t) => ({
datasetId: t.id({ required: true }),
diff --git a/packages/openneuro-server/src/graphql/schema/mutation.ts b/packages/openneuro-server/src/graphql/schema/mutation.ts
index 1c6dba844..670796243 100644
--- a/packages/openneuro-server/src/graphql/schema/mutation.ts
+++ b/packages/openneuro-server/src/graphql/schema/mutation.ts
@@ -28,6 +28,7 @@ import {
MetadataInput,
SummaryInput,
ValidatorInput,
+ MosaicInput
} from "./inputs"
import Mutation from "../resolvers/mutation"
@@ -122,6 +123,12 @@ builder.mutationType({
},
resolve: (root, args) => Mutation.updateValidation(root, args as never),
}),
+ updateMosaic: t.boolean({
+ args: {
+ mosaic: t.arg({ type: MosaicInput, required: true }),
+ },
+ resolve: (root, args) => Mutation.updateMosaic(root, args as never),
+ }),
updatePermissions: t.field({
type: DatasetPermissions,
args: {
@@ -332,6 +339,14 @@ builder.mutationType({
resolve: (root, args, ctx) =>
Mutation.revalidate(root, args as never, ctx),
}),
+ createMosaic: t.boolean({
+ args: {
+ datasetId: t.arg.id({ required: true }),
+ ref: t.arg.string({ required: true }),
+ },
+ resolve: (root, args, ctx) =>
+ Mutation.createMosaic(root, args as never, ctx),
+ }),
prepareRepoAccess: t.field({
type: RepoMetadata,
args: {
diff --git a/packages/openneuro-server/src/graphql/schema/snapshot.ts b/packages/openneuro-server/src/graphql/schema/snapshot.ts
index ce0a39559..a54b8ac7b 100644
--- a/packages/openneuro-server/src/graphql/schema/snapshot.ts
+++ b/packages/openneuro-server/src/graphql/schema/snapshot.ts
@@ -107,5 +107,9 @@ SnapshotRef.implement({
nullable: { list: true, items: true },
resolve: (obj) => SnapshotFields.contributors(obj),
}),
+ mosaic: t.boolean({
+ resolve: (obj, _args, ctx) =>
+ SnapshotFields.mosaic(obj, null, ctx) as never,
+ }),
}),
})
diff --git a/packages/openneuro-server/src/handlers/datalad.ts b/packages/openneuro-server/src/handlers/datalad.ts
index 222949bd9..001644b6d 100644
--- a/packages/openneuro-server/src/handlers/datalad.ts
+++ b/packages/openneuro-server/src/handlers/datalad.ts
@@ -4,6 +4,7 @@ import mime from "mime-types"
import { getFiles } from "../datalad/files"
import { getDatasetEndpoint, getDatasetWorker } from "../libs/datalad-service"
import { getDraftRevision } from "../datalad/draft"
+import { checkDatasetRead } from "../graphql/permissions"
/**
* Handlers for datalad dataset manipulation
@@ -120,3 +121,20 @@ export function gitRepo(req, res) {
)
return res.redirect(301, newUrl)
}
+
+/**
+ * Request a mosaic pdf for a dataset commit
+ */
+export const getMosaic = async (req, res) => {
+ const { datasetId, ref } = req.params
+ try {
+ await checkDatasetRead(datasetId, req.user?.id, req.user)
+ } catch {
+ res.status(403).send("You do not have access to read this dataset.")
+ return
+ }
+ const worker = getDatasetWorker(datasetId)
+ res.set("Content-Type", "application/pdf")
+ const uri = `${worker}/datasets/${datasetId}/mosaic/${ref}`
+ return request.get(uri).pipe(res)
+}
diff --git a/packages/openneuro-server/src/models/mosaic.ts b/packages/openneuro-server/src/models/mosaic.ts
new file mode 100644
index 000000000..bd22f6774
--- /dev/null
+++ b/packages/openneuro-server/src/models/mosaic.ts
@@ -0,0 +1,21 @@
+import mongoose from "mongoose"
+import type { Document } from "mongoose"
+const { Schema, model } = mongoose
+
+
+/**
+ * Mosaic output collection
+ */
+export interface MosaicDocument extends Document {
+ id: string
+ datasetId: string
+}
+
+const mosaicSchema = new Schema({
+ id: { type: String, required: true },
+ datasetId: { type: String, required: true },
+})
+
+const Mosaic = model("Mosaic", mosaicSchema)
+
+export default Mosaic
diff --git a/packages/openneuro-server/src/routes.ts b/packages/openneuro-server/src/routes.ts
index 5b0618ac6..cd031ac30 100644
--- a/packages/openneuro-server/src/routes.ts
+++ b/packages/openneuro-server/src/routes.ts
@@ -129,6 +129,12 @@ const routes = [
url: "/datasets/:datasetId/objects/:key",
handler: datalad.getObject,
},
+ {
+ method: "get",
+ url: "/datasets/:datasetId/mosaic/:ref",
+ middleware: [noCache, jwt.authenticate],
+ handler: datalad.getMosaic,
+ },
// Authentication routes
diff --git a/services/datalad/datalad_service/app.py b/services/datalad/datalad_service/app.py
index bd46032b9..dfd3be841 100644
--- a/services/datalad/datalad_service/app.py
+++ b/services/datalad/datalad_service/app.py
@@ -25,6 +25,7 @@
from datalad_service.handlers.upload import UploadResource
from datalad_service.handlers.upload_file import UploadFileResource
from datalad_service.handlers.validation import ValidationResource
+from datalad_service.handlers.mosaic import MosaicResource
from datalad_service.handlers.git import (
GitRefsResource,
GitReceiveResource,
@@ -123,6 +124,7 @@ def create_app():
datasets = DatasetResource(store)
dataset_draft = DraftResource(store)
dataset_validation = ValidationResource(store)
+ dataset_mosaic = MosaicResource(store)
dataset_history = HistoryResource(store)
dataset_drop = DropResource(store)
dataset_description = DescriptionResource(store)
@@ -155,6 +157,7 @@ def create_app():
app.add_route('/datasets/{dataset:dataset}/drop', dataset_drop)
app.add_route('/datasets/{dataset:dataset}/description', dataset_description)
app.add_route('/datasets/{dataset:dataset}/validate/{hexsha}', dataset_validation)
+ app.add_route('/datasets/{dataset:dataset}/mosaic/{hexsha}', dataset_mosaic)
app.add_route('/datasets/{dataset:dataset}/reset/{hexsha}', dataset_reset_resource)
app.add_route('/datasets/{dataset:dataset}/fsck', dataset_fsck_resource)
app.add_route('/datasets/{dataset:dataset}/info', dataset_info_resource)
diff --git a/services/datalad/datalad_service/handlers/mosaic.py b/services/datalad/datalad_service/handlers/mosaic.py
new file mode 100644
index 000000000..84c803a68
--- /dev/null
+++ b/services/datalad/datalad_service/handlers/mosaic.py
@@ -0,0 +1,46 @@
+import logging
+import falcon
+import os
+import aiofiles
+import pygit2
+
+from datalad_service.tasks.mosaic import create_mosaic, get_mosaic_path
+
+
+class MosaicResource:
+ def __init__(self, store):
+ self.store = store
+
+ async def on_get(self, req, resp, dataset, hexsha):
+ try:
+ repo = self.store.get_dataset_repo(dataset)
+ commit, _ref = repo.resolve_refish(hexsha)
+ mosaic_path = get_mosaic_path(dataset, repo, commit)
+ except (KeyError, pygit2.GitError, pygit2.InvalidSpecError):
+ resp.media = {'error': 'mosaic not found'}
+ resp.status = falcon.HTTP_NOT_FOUND
+ return
+ if os.path.exists(mosaic_path):
+ resp.status = falcon.HTTP_OK
+ fd = await aiofiles.open(mosaic_path, 'rb')
+ resp.set_stream(fd, os.fstat(fd.fileno()).st_size)
+ else:
+ resp.media = {'error': 'mosaic not found'}
+ resp.status = falcon.HTTP_NOT_FOUND
+
+ async def on_post(self, req, resp, dataset, hexsha):
+ """Create a mosaic for a given commit"""
+ if dataset and hexsha:
+ try:
+ dataset_path = self.store.get_dataset_path(dataset)
+ # Queue the mosaic but don't block on the request
+ await create_mosaic.kiq(dataset, dataset_path, hexsha, req.cookies)
+ resp.status = falcon.HTTP_OK
+ except Exception:
+ logging.exception(
+ 'Mosaic task enqueue failed for dataset %s', dataset
+ )
+ resp.status = falcon.HTTP_INTERNAL_SERVER_ERROR
+ else:
+ resp.media = {'error': 'Missing or malformed dataset parameter in request.'}
+ resp.status = falcon.HTTP_UNPROCESSABLE_ENTITY
diff --git a/services/datalad/datalad_service/tasks/mosaic.py b/services/datalad/datalad_service/tasks/mosaic.py
new file mode 100644
index 000000000..9b6bc58d9
--- /dev/null
+++ b/services/datalad/datalad_service/tasks/mosaic.py
@@ -0,0 +1,118 @@
+import os.path
+from pathlib import Path
+import logging
+import bidsmosaic
+import requests
+import pygit2
+
+from datalad_service.config import GRAPHQL_ENDPOINT, DATALAD_DATASET_PATH
+from datalad_service.broker import broker
+from datalad_service.common.redis import redis_client
+
+from datalad_service.common.git import git_show_content
+
+logger = logging.getLogger('datalad_service.' + __name__)
+
+
+def get_mosaic_path(dataset_id, repo, commit):
+ """Return path of a mosaic pdf file."""
+ try:
+ # Get tag if exists
+ label = repo.describe(
+ committish=commit,
+ max_candidates_tags=0,
+ describe_strategy=pygit2.enums.DescribeStrategy.TAGS,
+ )
+ except (KeyError, pygit2.GitError):
+ label = str(commit.id)[0:8]
+
+ mosaic_dir_path = Path(DATALAD_DATASET_PATH) / 'mosaics' / dataset_id
+ return mosaic_dir_path / f'{dataset_id}-{label}_mosaic.pdf'
+
+
+def mosaic_mutation(dataset_id, ref):
+ """
+ Return the OpenNeuro mutation to update the snapshot mosaic.
+ """
+ mosaicInput = {
+ 'datasetId': dataset_id,
+ 'id': ref,
+ }
+ return {
+ 'query': 'mutation ($info: MosaicInput!) { updateMosaic(mosaic: $info) }',
+ 'variables': {
+ 'info': mosaicInput,
+ },
+ }
+
+
+def _stream_opener(repo, ref, relpath):
+ """Return a function that runs git_show_content() and returns just the stream."""
+
+ async def opener():
+ stream, _size = await git_show_content(repo, ref, relpath)
+ return stream
+
+ return opener
+
+
+def _is_anat(path):
+ """True for a raw anatomical nifti, ie sub-*/**/anat/*.nii[.gz]."""
+ return (
+ path.startswith('sub-')
+ and os.path.basename(os.path.dirname(path)) == 'anat'
+ and path.endswith(('.nii', '.nii.gz'))
+ )
+
+
+def create_anat_files_dict(repo, commit):
+ """Return {datatype: [(relpath, opener), ...]} for all anatomical images.
+ Used as input for create_mosaic_pdf_async()."""
+ hexsha = str(commit.id)
+ index = pygit2.Index()
+ index.read_tree(commit.tree)
+ anat = sorted(entry.path for entry in index if _is_anat(entry.path))
+ return {'Anatomical': [(path, _stream_opener(repo, hexsha, path)) for path in anat]}
+
+
+@broker.task
+async def create_mosaic(dataset_id, dataset_path, ref, cookies=None):
+ async with redis_client() as client:
+ lock = client.lock(f'mosaic-lock:{dataset_id}:{ref}', timeout=60 * 60 * 4)
+ if await lock.acquire(blocking=False):
+ try:
+ repo = pygit2.Repository(str(dataset_path))
+ commit, _ref = repo.resolve_refish(ref)
+
+ files_dict = create_anat_files_dict(repo, commit)
+ if not any(files_dict.values()):
+ logger.info(
+ 'No anatomical images for %s %s; skipping mosaic',
+ dataset_id,
+ ref,
+ )
+ return
+
+ out_file_path = get_mosaic_path(dataset_id, repo, commit)
+ out_file_path.parent.mkdir(parents=True, exist_ok=True)
+
+ await bidsmosaic.create_mosaic_pdf_async(
+ str(out_file_path),
+ files_dict,
+ downsample=2,
+ strict=True,
+ )
+
+ if out_file_path.exists():
+ r = requests.post(
+ url=GRAPHQL_ENDPOINT,
+ json=mosaic_mutation(
+ dataset_id,
+ ref,
+ ),
+ cookies=cookies,
+ )
+ if r.status_code != 200 or 'errors' in r.json():
+ raise Exception(r.text)
+ finally:
+ await lock.release()
diff --git a/services/datalad/pyproject.toml b/services/datalad/pyproject.toml
index 1883634db..e0a3c38e2 100644
--- a/services/datalad/pyproject.toml
+++ b/services/datalad/pyproject.toml
@@ -6,6 +6,7 @@ requires-python = ">=3.13"
dependencies = [
"aiofiles>=24.1.0",
"aioshutil>=1.5",
+ "bids-mosaic>=0.2.0",
"bidsschematools>=1.0.10",
"boto3>=1.42.95",
"charset-normalizer>=3.4.7",
diff --git a/services/datalad/uv.lock b/services/datalad/uv.lock
index 7eeb78774..b17d04446 100644
--- a/services/datalad/uv.lock
+++ b/services/datalad/uv.lock
@@ -1,6 +1,14 @@
version = 1
revision = 3
requires-python = ">=3.13"
+resolution-markers = [
+ "python_full_version >= '3.14' and sys_platform == 'win32'",
+ "python_full_version >= '3.14' and sys_platform == 'emscripten'",
+ "python_full_version >= '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'",
+ "python_full_version < '3.14' and sys_platform == 'win32'",
+ "python_full_version < '3.14' and sys_platform == 'emscripten'",
+ "python_full_version < '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'",
+]
[[package]]
name = "acres"
@@ -158,6 +166,36 @@ wheels = [
{ url = "https://files.pythonhosted.org/packages/3a/2a/7cc015f5b9f5db42b7d48157e23356022889fc354a2813c15934b7cb5c0e/attrs-25.4.0-py3-none-any.whl", hash = "sha256:adcf7e2a1fb3b36ac48d97835bb6d8ade15b8dcce26aba8bf1d14847b57a3373", size = 67615, upload-time = "2025-10-06T13:54:43.17Z" },
]
+[[package]]
+name = "bids-mosaic"
+version = "0.2.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+ { name = "matplotlib" },
+ { name = "nibabel" },
+ { name = "nilearn" },
+ { name = "numpy" },
+ { name = "pillow" },
+ { name = "pybids" },
+ { name = "reportlab" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/f6/10/1e5dc5f23ec9d5dc688e0a582394cfd577137d0c0a6fd7058924f23854a5/bids_mosaic-0.2.0.tar.gz", hash = "sha256:cbef11e15ae4d2547c015b214467bad78b68d608f9c77604d731ac05aa0fcbbf", size = 12629, upload-time = "2026-08-06T22:44:59.054Z" }
+wheels = [
+ { url = "https://files.pythonhosted.org/packages/ef/2b/1768e24a3d32c0e2c683f49bdd3e96a56bbdb87d92437369764acddb6aa5/bids_mosaic-0.2.0-py3-none-any.whl", hash = "sha256:1c26ed26d261f93a55da3721c4974d62e2d967946f89d7513e9cfa0df00ef1d0", size = 8976, upload-time = "2026-08-06T22:44:58.099Z" },
+]
+
+[[package]]
+name = "bids-validator"
+version = "1.14.7.post0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+ { name = "bidsschematools" },
+]
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