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MACSQuant® Instrument quick guide
File management
Description
In addition to automatically saving data files, the
MACSQuantify™ Software enables users to create and save
various other files for efficient use of the MACSQuant®
Instrument. These files include analysis templates and
instrument settings. This quick guide contains brief descriptions
of these types of files as well as guides users in transferring
these files from the MACSQuant Instrument to remote
directories for use on their personal computers for data analysis.
File types in the MACSQuantify Software
Analysis templates
An analysis template is a pre-defined layout for acquired
data and is composed of plots, statistics or tables, gating
strategies, and defined plot and region properties, such as
region names and displayed statistics. Analysis templates
are data independent and when opened will not contain
any data, but can be used to insert data for analysis.
Analysis templates are saved in the ‘Analyses’ folder within
the MACSQuantify Software folder structure. The must
be selected to save an analysis template.
Figure 1: Example of an analysis template with the associated
hierarchical gating strategy (pasted for reference)
Experiments
An experiment consists of everything that has been
programmed into the ‘Experiment’ tab, including any
formatting of a Chill Rack, specific annotations, and any
selections in the autolabel or settings tabs. Experiment
files are located in ‘Experiments’ folder within the
MACSQuantify Software folder structure.
Instrument settings
An instrument setting file consists of PMT voltage values,
channel scales, compensation matrix, height, width, and
trigger selections that are important for data acquisition of
specific experiments. Saved instrument settings have very
finite instrument setting values, that can be repeatedly
used if applicable for your experiment, but should not be
used long term and should be updated in accordance with
instrument performance. Instrument settings are saved
in ‘Device’ folder within the MACSQuantify Software
folder structure.
Figure 2: Example of information saved in instrument settings
Workspaces
A workspace file is all encompassing, and represents a
master file including information from the following file
types: analysis templates, instrument settings, and
experiments. A workspace file will also save a link to any
data that was listed in the ‘Samples’ tab at the time of
saving the workspace file. Workspaces are recommended
for use on the PC version of the MACSQuantify Software.
Any associated data files saved as links with the workspace
must still exist in the same location as they were when the
workspace was saved! Workspace files are saved in the ‘prj’
folder within the MACSQuantify Software folder structure.
To save a workspace, make sure the is not selected.
Data management
It is recommended that data be backed up to a remote
location and that data files are removed from the hard drive
of the MACSQuant Instrument on a regular basis. These
remote locations can be USB thumb drives, external hard
drives, network locations, local PC, etc. Copies of the data
files as well as other files can be saved to remote locations
using two methods, ‘Backup’ or ‘Copy’. These functions
just place a copy in the remote location chosen, but does
not automatically delete the files from the MACSQuant
Instrument.
Refer to the respective chapters of the MACSQuantify
Software 2.5 user guide for more information.
Performing file back up
1. If using a USB thumb drive to transfer data, insert
into available USB port and wait a few seconds for
the device to be recognized.
2. Click on the icon.
3. Choose the location for file backup.
4. If a network folder is the backup destination, enter
password when prompted.
5. Select ‘all files’ or ‘all data files’ when/if prompted.
6. When back up is complete confirmation is listed in the
dialog box.
7. When the backup is performed again, all previously
backed up .mqd data files will be deleted if ‘delete
cloned files’ is selected when prompted. All .fcs files
will need to be deleted manually through the copy
function (see below).
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Transferring files using the copy function
1. If using a USB thumb drive to transfer data, insert
into available USB port and wait a few seconds for
the device to be recognized.
2. Open the ‘Copy’ function from the ‘File’ menu
3. Choose the remote location from the available
dropdown menu.
4. If using a network location to transfer file,
enter password when prompted.
5. In the file folder windows, select the files or folders
to be copied. Data files as well as other files, e.g.,
instrument settings and templates can be copied.
6. Select ‘Copy’.
7. When all files are copied, a report dialog box appears.
You can close the box to perform other copy or deletion
functions.
8. If using a USB thumb drive, the option to ‘Close and
eject’ is available. ‘Close and eject’ will allow safe
removal of the USB device. If eject is not chosen at this
time, go to ‘Tools’ tab and select ‘Remove external
media’ to stop the USB device safely.
9. To remove files that have been copied, the delete
button in the copy dialog box can be used. Folders
or individual files can be deleted. Also .fcs files
can be deleted by this function.
 Note: Please confirm that files have been copied
appropriately to the remote location prior to deletion.
Figure 3: ‘Copy’ function window
Are you in need of additional assistance?
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