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

• 1. Create a directory for each experimental prep, on which you performed a series of experimental measurements. Our tools expect this to be in the form of a long date, e.g., 2013-12-25 for Dec 25, 2013. Even if you've studied a prep over multiple days, choose one day for labeling the data.

  2. Create a separate subdirectory for each epoch of experimental recording or stimulation you performed. In our lab, we use 't00001', 't00002', 't00003', for these, although they can be any string that lacks spaces or special characters. It is best if the alphabetical/numerical order corresponds to the order in which the recordings were made, to take advantage of full features. They do not have to be sequential, just in alphabetical/numerical order.

  3. Place your TIFF stack files. The TiffStackFitz platform assumes files will be named stack_cC_N_1.tiff where C is the channel number and N is the sequence number of the tiff stack.

  4. Create a  reference.txt file for each subdirectory, which tells our software what is stored in that directory. An example reference.txt that you can modify is attached to this page. The first row must be "name<tab>ref<tab>type<return>", which indicates the fields. The additional rows should have the type of recording that was made.  For example: "tp<tab>1<tab>prairietp<return>" indicates that a set of imaging data is present. Currently, the type must be prairietp even if the data was acquired on a different system.  Each imaging location should have a unique reference number.  For example, if you made 2 measurements of the same tissue, and the data are in subdirectories t00001 and t00002, then the same reference number should be used in both t00001 and t00002.  Suppose you then moved your microscope to go to a different location in the preparation and recorded more data in t00003. You should use a different reference number in t00003 to indicate that the program should not attempt to merge the data in t00003 with that in t00001 and t00002. 

  5. Add a header.tiffstack file. The first row must be "property<tab>value<return>" and the second row should be "FrameRate<tab>30<return>". Where 30 is written, put whatever frame rate is used for your system (it might be 30 or another value). 

Converting data recorded with another system

• 6. Create a directory for each experimental prep, on which you performed a series of experimental measurements. In our lab, we generally do one experiment per day, and use the date as the label. You might create a directory 2013-12-25 for Dec 25, 2013.

  7. Create a separate subdirectory for each epoch of experimental recording or stimulation you performed. In our lab, we use 't00001', 't00002', 't00003', for these, although they can be any string that lacks spaces or special characters. It is best if the alphabetical/numerical order corresponds to the order in which the recordings were made, to take advantage of full features.

  8. Place one set of image files in each of these subdirectories. For example, if you have an image stack from a particular recording epoch called imageStack.tif, please it in a unique folder ('t00001' for example). Make sure you do not have 2 sets of image files from different times in the same folder.

  9. Create a  reference.txt file for each subdirectory, which tells our software what is stored in that directory. An example reference.txt that you can modify is attached to this page. The first row must be "name<tab>ref<tab>type<return>", which indicates the fields. The additional rows should have the type of recording that was made.  For example: "tp<tab>1<tab>prairietp<return>" indicates that a set of imaging data is present. Currently, the type must be prairietp even if the data was acquired on a different system.  Each imaging location should have a unique reference number.  For example, if you made 2 measurements of the same tissue, and the data are in subdirectories t00001 and t00002, then the same reference number should be used in both t00001 and t00002.  Suppose you then moved your microscope to go to a different location in the preparation and recorded more data in t00003. You should use a different reference number in t00003 to indicate that the program should not attempt to merge the data in t00003 with that in t00001 and t00002.