Most common options for optical imaging data analysis:


1. Run iman on the raw stream files:

iman –s –D –T1 [-t] t_abc.1x00 where abc is a code for the date and 1 is the experiment number and x is the run number (0-z)

Iman takes –F2 to do orientation out of a 360 direction of movement stimulus.

Iman takes –R1 for episodic stimulus analysis

Iman –w8 to view green files

Running iman with the –t option allows you to look at the power spectrum of any selected point, and at the stimulus phase sawtooths.

All interactive commands except saving the map are given in the interactive window.

In all cases iman produces a mapraw file with a name like t_abc.1x00.mapraw2_46_58_2641dt1, with the numbers telling about the frames and cycles included in the analysis


2. mapans can be used to normalize the mapraw files generated by iman

mapans –i –o6 t_abc.1x00.mapraw2_46_58_2641dt1 generates a file of the same name with the suffix _a

To select an area for normalization, hit ‘c’ (for ‘crop’) in the interactive window (a grey scale window) and trace a region of interest for normalization (left mosue button to mark points, right to close region), and then hit ‘n’ (for normalize). If you don’t crop first but just hit ‘n’, then it uses the whole image for normalization. If you like it, hit ‘c’ and then ‘c’ again to normalize the whole image according to the values obtained from the region of interest.

All commands are given in the interactive window. ‘S saves the file. ‘Q’ quits.

With excellent quality images, normalization is not requires, but it generally does not hurt if the full range of phases is present in the response, or if there is enough off-brain area with random pixels in the image

3. mapamn2 can be used to compute the average image from two normalized images that were made from stimuli moving or rotating in the opposite directions (time-reversed stimuli).

mapanm2 –i16 file1 file2 where these files are the output of mapans.

Orientation: file1: CCW (-1), file2: CW (+1).

Topography: file1: 0 deg, file2: 180 deg; or else file1: 90 deg, file2: 270 deg

SF, TF: file 1: ascending, file2: descending

All commands are given in the interactive window. ‘S saves the file. ‘Q’ quits.

4. To print pictures, mapans file1 where file1 is the output of iman (ends with dt1) or mapans (ends with dt1_a)

Press <RETURN> in command window. In response to the prompt “Save image?” type y for both the phase and amplitude maps, or Y if you want just the phase map. It will output a string with suggested filename and output method in the form “t_abc.xxxxxxx.ps/VCPS”. Copy and paste that string, then press enter to save the PostScript file.

To view the file, gv file1 where file1 is t_abc.xxxxxxx.ps. To print in color, lpr –P830c file1 or for black&white use 811 or 830 instead of 830c.