Step 5: Concluding the acquisition

Once the requested number of sections have been acquired, the acquisition will stop automatically and the laser and PMTs will be switched off. If this is an auto-ROI acquisition, it will stop automatically if no tissue found.

Stopping an acquisition early

Should you wish to stop the acquisition earlier, hit the "Stop" button in the acquire GUI. You will then be presented with a window asking you if you want to halt right now or at the end of the current section. There is also a checkbox indicating if you want the acquisition to be marked as "Finished". If this is checked, a signal is sent to syncAndCrunch (a file called FINISHED is made in the sample directory) to to start stitching. Note that after manually halting the acquisition, the PMTs are turned off but the laser remains on. If you wish to turn off the laser, enter the laser GUI and press "Turn Off".

Post-acquisition tasks

The following are common tasks you will need to perform on the analysis PC after acquisition is complete.

• You will optionally compress the raw unstitched tiles for long-term storage with the compressRawData command line tool.

• Crop excess imaged area if this is a single sample using the stitchit.sampleSplitter tool. Cropping is especially important if you performed an auto-ROI acquisition as the algorithm sometimes images an excessively large area in a small number of sections and this greatly bloats the stitched image size compared to the unstitched raw tiles.

• If you imaged multiple brains you will use the stitchit.sampleSplitter to split these into separate data directories.

• Copy data to a remote server and delete the local copy on the analysis PC with the transferToServer command line tool..

The Python package btpytools exists for assisting with data compression and transferring data to a remote server.