Supported image types

Supported file formats

Our filesystem supports any file format supported by Bioformats (see limitations below). You can see their supported formats here.

Most battle-tested formats

Some formats have been used and tested more extensively on Biodock. If you can export files in multiple formats, you should use these.

• .tiff/.tif

• .svs

• .czi (with limitations below)

• .lif (with limitations below)

• .png

• .jpg/.jpeg

• ome.tiff

• mrxs (see how to upload below)

• vsi (see how to upload below)

Special format uploads: mrxs and vsi

MRXS and VSI files are complex files that need multiple accompanying folders and files in order to be appropriately opened in Biodock and other software.

See below how these files needs to be structured before you upload them to Biodock.

MRXS format set up

VSI format set up

Once you have these files set up correctly, you can upload them to Biodock using "Browse folders"

Select the top level file and click upload

Confirm the file format is correct. In this example this is one VSI file

Processing large images takes time, so please give few minutes before it is finished. The upload starts off as yellow progress bar, when the progress bar turns blue, you can close the window.

Yellow progress bar

Blue progress bar

General limitations

Time series

Biodock does not support time series data within a single file, time series traces on the Dashboard, or tracking objects between timepoints. If you would like to analyze on time-series data, you can separate each time point into it's own folder. This will allow you to compare metrics across time points on the dashboard.

3D data

Biodock only supports training and analysis on 2D (but multichannel supported) images. This means that Biodock does not yet support volumetric metrics. If you have 3D images, you can currently:

• Use max projection images

• Pick z stacks to do analysis

• Run training/analysis across each of your z-dimension images