How do I organize my external 2-photon or confocal data to be analyzed by the VHlabtools?

The easiest way is to add the folder structure that the VHlabtools expects (Data formats).

Our directory structure in brief

Please see the following page for a description of our experiment directory structure.

Converting data recorded with PrairieView software

For example, suppose you have Prairie time series data stored in your experiment directory 2010-09-19 as mydir-001, mydir-002, mydir-003, myotherdir-001, and mythirddir-001.

Then the easiest thing to do would be to do the following:

1) In your experiment folder 2010-09-19 (or whatever it is), add directories mydir, myotherdir, and mythirddir

2) Now you need to add reference.txt files to these new folders so that our software will recognize their contents.  The actual way you do this will depend on the data you have collected.  Suppose that mydir-001, mydir-002, mydir-003, and myotherdir-001 were all collected with the microscope positioned at the same location, while mythirddir-001 was recorded somewhere else.  Then you'd need to tell our software of this fact by using the same "name/reference" pair in the reference.txt file.  In the example here, you could make the reference.txt files in mydir-001, mydir-002, mydir-003, and myotherdir-001 the same, with the contents:

name    <tab>    ref    <tab>    type    <return>

tp    <tab>    1    <tab>    prairietp<return>

while the reference.txt file in mythirddir-001 should be:

name    <tab>    ref    <tab>    type    <return>

tp    <tab>    2    <tab>    prairietp<return>

Note that there should be no spaces between the fields, just tabs or returns as indicated.  The type of prairietp tells our software to expect 2-photon data in the PrairieView format; tp is just an arbitrary name field (this field comes in handy if you have many electrodes and want to give them different names, though one would be unlikely to use many 2-photon microscopes simultaneously!), and reference indicates the position reference.  Using the same number 1 for  mydir-001, mydir-002, mydir-003, and myotherdir-001 indicates that these recordings are at the same position, and that our software should try to combine information about recordings and cell positions across these recordings.  Using a new reference number indicates that the same type of recording is being made, but at a new location that should not be analytically combined with recordings with different reference numbers.

Converting tiff stacks from Fitz lab

Converting data recorded with another system