SMAP

File › Load · version 2

Read a SMAP _sml.mat file.

What it does

Opens the _sml.mat files that SMAP (Ries 2020) writes, so that data fitted or analysed in SMAP can be analysed here. It reads the localizations and the camera's pixel size; nothing else of SMAP's session comes across.

Use it rather than Auto for a .mat file whose name does not end in _sml.mat: this plugin reads it as SMAP's format whatever it is called. Both the older MATLAB files and the -v7.3 ones (which are HDF5 inside) are read.

How it works

1. The localizations. SMAP keeps its table in saveloc.loc, one field per column. Each field becomes a column, renamed to this program's name where there is one (the table under In detail) and kept under its own name where there is not. A few columns are left behind: filenumber, which is given again when the file is added to the session, and the columns this program never reads (xnmf, ynmf, xpixf, ypixf, xpixerr, ypixerr, PSFypix).

2. Frames from zero. MATLAB counts from 1, so the frame numbers are shifted down by one: SMAP's frame 1 is frame 0 here.

3. The camera. The pixel size (cam_pixelsize_um) is read from the first file's info, and in a -v7.3 file also the frame count, the conversion, the offset and the EM gain. They are kept in the table's metadata under smap.

4. Linking. As with every loader, the blinks are then linked (see Auto).

What happened to the columns of a file shaped like SMAP's, as this plugin read it: renamed where this program has a name for the quantity, kept as they are where it has none, and dropped where nothing here reads them.

In detail

The renames (SML_COLUMNS):

frame, channel and iterations keep their names. Every other field – numberInGroup, a column SMAP's own plugins added, a derived field – comes across under its SMAP name. In particular SMAP's numberInGroup is not this program's n_in_group: that is written by the linking here.

Types. The frame is

stored as a 64-bit integer; channel and iterations become 32-bit integers, and every other double-precision column becomes single precision, which halves the memory and loses nothing a localization can carry.

Units. SMAP stores positions in nanometres, and the table is marked as being in nanometres. Its pixel columns (xpix, ...), if the file has them, come across as x_pix, ... beside the nanometre ones.

Which files. The reader looks for saveloc in the file: a .mat without it is not a SMAP localization file and is refused. A file that held several SMAP files at once is read as one, since its filenumber is among the columns left behind.

Output

The table, added to the session as a file of its own (or appended, with add to the open files). The text says how many localizations were read and, if they were linked, how many blinks they make. The load is written into the session's history with its settings.

Differences from SMAP

Based on SMAP's Loader_sml (Ries 2020). The main changes:

• Only the localizations and the camera numbers are read. SMAP also restores the file's history, the ROI manager's sites and, when asked, the GUI parameters saved with it; those describe SMAP's own windows and plugins, which have no counterpart here.
• A file that holds several SMAP files is read as one table.
• Frames count from 0, and the columns are renamed to this program's names.

References

• Ries J. SMAP: a modular super-resolution microscopy analysis platform for SMLM data. Nat Methods 17, 870 (2020). doi:10.1038/s41592-020-0938-1 – the program whose files this reads.

Parameters