Reviewing these resources helps you use MapMyCells to its full potential:
- MapMyCells intro page
- MapMyCells tutorial notebook
- Input file requirements, limits, and creation
- Available cell type references, algorithms, and output files
- In-depth MapMyCells output documentation
MapMyCells can be accessed in a variety of ways.
Access it via the information page linked on https://portal.brain-map.org/ highlighted below. You can also access it via Atlases and Data > Brain Knowledge Platform > MapMyCells via the header menu.
Alternatively, you can access MapMyCells via the Tools section in header menu on https://knowledge.brain-map.org/:
Lastly, go straight to MapMyCells via http://knowledge.brain-map.org/mapmycells/process/.
Select a file or drag it into the dotted-line area. Click the X next to the file to remove the uploaded file and start over.
More information about the file requirements and how to create a compatible h5ad file is available via the linked Learn about input file requirements, limits, and creation help page.
Select the mapping algorithm and reference taxonomy from the drop down menus.
Additional information about the taxonomies and algorithms is available via the Learn about available cell type references, algorithms, and output files help page.
Click the START button to initiate the mapping process.
We estimate the approximate runtime of the mapping, e.g. 5 minutes.
A progress indicator illustrates the different stages of the process and the overall progress.
IMPORTANT: Do NOT close the browser tab while the mapping is running. Your progress will be lost.
Once the mapping concludes, download your results via the DOWNLOAD RESULTS button.
NOTE: The download triggers in a pop-up message. Please ensure that you allow pop-ups for the MapMyCells page.
IMPORTANT: Once you close the browser tab, all files will be deleted.