Why does Autoquant reject xml input (for implentation of AutoQuant Connect)?

Hi everyone,

I am attempting to automate batch processing (3D deconvolution) using Autoquant Connect, but I have run into a snag and would really appreciate any advice.

 

Some details:

 I am trying to use Autoquant Connect to send files to Autoquant for processing. I originally used some sample files from previous tests done a by a colleague and managed to get the process working. By process I mean

-          Write xml file containing data required for Autoquant to perform deconvolution

-          Use command prompt to send xml data to Autoquant to perform the processing.

 We now have our own 2 photon microscope up and running and I have acquired some images to process by using the process and xml file structure above. For the image acquisition I use Prairie View, and for a test batch I have acquired:

-          3 areas/regions 

-          Of 14 slices each 

-          Each region repeated 4 times

The folder structure output from Prairie View is 

-          Main folder with all regions

                     o   Folder containing Region 1

                                 §  Z stack 1 (14 slices)

                                 §  Z stack 2 (14 slices)

                                 §  Z stack 3 (14 slices)

                                 §  Z stack 4 (14 slices)

                    o   Folder containing  Region 2

                                §  Z stack 1 (14 slices)

                                §  Z stack 2 (14 slices)

                               §  Z stack 3 (14 slices)

                              §  Z stack 4 (14 slices)

                    o   Folder containing  Region 3

                             §  Z stack 1 (14 slices)

                             §  Z stack 2 (14 slices)

                             §  Z stack 3 (14 slices)

                             §  Z stack 4 (14 slices)

 

For the moment I use only one channel but in the future I plan to use at least 2.

The problem I am having now with the different structure is that Autoquant does not seem to like the specification of the Source File I put into the xml (for Autoquant Connect step).

I have tried:

-          Using the *.xml file output from Prairie View, there is one for each region

-          Specifying each .tif individually by specifying channel and frame as attributes in the source file tag

Both of these have not worked. The Result file ErrorDescription tag states: Error preparing deconvolution; code: 1. Unfortunately I have no way of knowing what code 1 means and so I am unable to debug logically without trying every random possibility of Source File input.

Essentially in the end I would like to send the entire main folder (containing all region folders containing all stacks and repetitions) to Autoquant to deconvolve in succession.

Thoughts anyone?

I would greatly appreciate any help/advice on this as it is really bottlenecking the subsequent processing I am working on. I can send example files of the generated xml as well as the code I have written if this would help.

Thanks,

Gabi

Answers

  • Hi Gabi,
    If possible, I would very much like to see the generated XML to see what might look off about it.

    Thanks,
    Andy
  • Hi Andy, 

    The files are attached in the email David CC'd you in on. 

    Please let me know if you received them or if I should send again.

    Thanks, 
    Gabi
  • It appears that they got lost in the process of adding me to that thread. Would you mind re-sending them? Thanks!
  • Thank you for sending the file; I'm glad we could resolve the issue.

    For anyone else that may be having issues with an AutoQuant Connect file, there were a couple of pointers that were relevant in this case.

    First, when specifying the SourceFile location attributes (TimePoint, Channel, and Frame), keep in mind that the locations are zero-indexed. You may have files with one-indexed names, like:
    c:\images\myexperiment_t1_ch1_z1.tif
    c:\images\myexperiment_t1_ch1_z2.tif

    but for the purposes of the SourceFile node, those will need to map to set locations starting from zero, like this:
    <SourceFile TimePoint="0" Channel="0" Frame="0">c:\images\myexperiment_t1_ch1_z1.tif</SourceFile>
    <SourceFile TimePoint="0" Channel="0" Frame="1">c:\images\myexperiment_t1_ch1_z2.tif</SourceFile>

    Second, the dimension nodes - ImageWidth, ImageHeight, FrameCount, ChannelCount, TimePointCount (in particular the last two) - are optional in cases where they can be taken from the SourceFile metadata, or are 1 in value. But they become necessary otherwise. When in doubt, include them - having them be redundant won't hurt anything.

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