Are mrxs really compatible?

[arkanoid87]

Hello!

pathcollab was super easy to setup using docker image: ghcr.io/pabannier/pathcollab:latest but mrxs slides seems not supported

...
2026-03-07T01:44:20.509038Z  INFO pathcollab_server::slide::local: Found 37 slides in "/slides"
2026-03-07T01:44:20.509612Z  WARN pathcollab_server::slide::local: Failed to open slide A-1-a: Failed to open slide: Failed to open "/slides/A-1-a.mrxs": Unsupported file format: /slides/A-1-a.mrxs
...

same file opens correctly with QuPath

[arkanoid87]

well, it seems it's just my slides not working.

I've downloaded Mirax2-Fluorescence-1.zip from openslide test file, and it works in pathcollab, so it must be something specific of my files, but the logs are really generic about it

[arkanoid87]

the docker image runs openslides 3.4.1, which is pretty ancient. I've compiled latest master and it opens my mrxs correctly

[arkanoid87]

I've rebuilt the image adding step to build OpenSlide from source, and now all my slides opens correctly in PathCollab

# Frontend
FROM oven/bun:1.3-alpine AS frontend-builder
WORKDIR /app/web
COPY web/package.json web/bun.lock* ./
RUN bun install --frozen-lockfile
COPY web/ ./
RUN bun run build

# OpenSlide from source
FROM debian:bookworm-slim AS openslide-builder

RUN apt-get update && apt-get install -y \
    git \
    meson \
    ninja-build \
    pkg-config \
    libcairo2-dev \
    libgdk-pixbuf2.0-dev \
    libxml2-dev \
    libsqlite3-dev \
    libjpeg-dev \
    libopenjp2-7-dev \
    libtiff5-dev \
    zlib1g-dev \
    && rm -rf /var/lib/apt/lists/*

RUN git clone --depth 1 https://github.com/openslide/openslide.git /tmp/openslide && \
    cd /tmp/openslide && \
    meson setup builddir --prefix=/usr/local --buildtype=release && \
    meson compile -C builddir && \
    meson install -C builddir --destdir=/install

# Backend
FROM rust:1.89-slim-bookworm AS backend-builder
WORKDIR /app

RUN apt-get update && apt-get install -y \
    pkg-config \
    libssl-dev \
    libclang-dev \
    protobuf-compiler \
    libcairo2-dev \
    libgdk-pixbuf2.0-dev \
    libxml2-dev \
    libsqlite3-dev \
    libjpeg-dev \
    libopenjp2-7-dev \
    libtiff5-dev \
    zlib1g-dev \
    && rm -rf /var/lib/apt/lists/*

# Copy OpenSlide
COPY --from=openslide-builder /install/usr/local /usr/local
RUN ldconfig

COPY Cargo.toml Cargo.lock* ./
COPY server/Cargo.toml server/build.rs ./server/
COPY proto ./proto

RUN mkdir -p server/src \
    && echo "fn main() {}" > server/src/main.rs \
    && echo "" > server/src/lib.rs

RUN cargo build --release --package pathcollab-server
RUN rm -rf server/src

COPY server/src ./server/src
RUN touch server/src/main.rs server/src/lib.rs \
    && cargo build --release --package pathcollab-server

# Runtime
FROM debian:bookworm-slim
WORKDIR /app

RUN apt-get update && apt-get install -y \
    ca-certificates \
    curl \
    libcairo2 \
    libgdk-pixbuf2.0-0 \
    libxml2 \
    libsqlite3-0 \
    libjpeg62-turbo \
    libopenjp2-7 \
    libtiff6 \
    zlib1g \
    && rm -rf /var/lib/apt/lists/*

COPY --from=openslide-builder /install/usr/local /usr/local
RUN ldconfig

COPY --from=backend-builder /app/target/release/pathcollab /usr/local/bin/pathcollab
COPY --from=frontend-builder /app/web/dist /app/static

RUN useradd -r -s /bin/false pathcollab \
    && mkdir -p /slides /overlays \
    && chown -R pathcollab:pathcollab /app /slides /overlays

USER pathcollab

EXPOSE 8080

ENV RUST_LOG=pathcollab=info,tower_http=info \
    HOST=0.0.0.0 \
    PORT=8080 \
    SLIDES_DIR=/slides \
    OVERLAY_DIR=/overlays \
    STATIC_FILES_DIR=/app/static \
    SLIDE_SOURCE=local

HEALTHCHECK --interval=30s --timeout=3s --start-period=5s --retries=3 \
    CMD curl -f http://localhost:8080/health || exit 1

VOLUME ["/slides", "/overlays"]

CMD ["pathcollab"]