AutoQuant General Discussions — Media Cybernetics Image Analysis Forums

is this forum only about matters no offtopic

josefromeo — Thu, 04 Jan 2024 13:27:00 +0000

i was going through different topics of media like news and journalist and this forum came in front of me as media so can post about about any news and media related thing or it dosent allow people to talk about offtopic things

autoquant decon batch error

chungd3 — Thu, 14 Dec 2023 19:48:38 +0000

I am trying to perform autoquant decon using batch selection. However, whenever I do the batch decon, the error shows that x, y and z calibration must be greater than zero, although I set these values in the spatial calibration section. Running the decon on individual image still works.

Measured PSF tool?

stanvitha — Wed, 10 May 2023 21:38:38 +0000

I am processing Light Sheet datasets, which requires measured PSF for 3D deconvolution.

Where is the PSF extractor/distiller tool, if there is one?

I have the beads dataset, just not sure how to go about averaging PSF from multiple beads.I guess I could just pick a single bead and crop, but averaging multiple PSFs may be better.

Huygens has the PSF distiller, so I expect Autoquant has something similar, just cannot find it.

Thanks!

Instrument settings - objective database entry not properly applied?

stanvitha — Tue, 30 Aug 2022 21:41:43 +0000

I created a new entry in the objective database (in the Instrument section of data manager).

When I load a dataset and select the saved objective setting from the database, it loads the info (mag, NA, immersion). So far so good:

As soon as I click "Apply" or anywhere else either in the Instrument tab in the software (like drag the image window), the objective NA, immersion and magnification revert to some other value:

it seems that the Instrument tab is not designed to enter that information for the current dataset. If I go to Summary, and select the objective again, seemingly nothing happens (objective name is correct, but the parameters did not update):

After I click Apply, all is well, and the NA and immersion and mag are applied.

HOWEVER, if I selected the objective in the "Instruments' tab, and then go to the "summary tab", I see the correct objective name listed, but the parameters (NA, immersion, ) did not update. If I click "Apply", nothing changes, the wrong/old parameters are still in there. The "Apply " button in Summary tab only updates the info if the objective is selected in the scroll-down list.

after clicking "Apply":

Three short questions:

1) is the Objective database behavior in the Instruments tab how it should be? I expected to be able to select an objective and apply its properties to the dataset from there.

2) The list of objectives in the Instruments tab is sorted alphabetically, it seems, while the list of the same objectives in the Summary tab is sorted in some other manner (maybe latest entries at the bottom). it is somewhat irritating to have it this way. Can we please have the lists sorted the same way?

3) Would it be possible to have the objective properties loaded/applied as soon as the objective is selected? There are many objectives in the database that just have a general type, so it takes one extra click to see if the HC Plan Apo si a 10x, or a 40x, or something else.

Thanks

Stan

Turning channels display on/off in AQX3

stanvitha — Mon, 29 Aug 2022 16:46:39 +0000

Howdy,

I have a 2-channel image stack (GFP, Cy5) that is shown in Red and Green overlay. i would like to hide one of the channels to have just one channel displayed. I knew how to do it in X2 (AQX2 shows a data tree with channels separately and a checkbox for each channel) The X3 is not showing the channels separately in Data Managers in a tree display.

Is there a new trick to it?

On a related note, I how would I split a 2-channel image stack to two separate stacks in AQ3?

Thanks!

Stan Vitha

Texas A&M University

Microscopy and Imaging Center

Attempting to use the alignment tool- AutoQuant X 3.1.2

microscopyra — Mon, 01 Oct 2018 21:41:25 +0000

Hi! Not sure if this is the correct place for this kind of question, but if not, please point me in the appropriate direction!
I have been attempting to run an alignment on a 2 color fluorescent Z stack where the mouse jumped a bit during one of the frames (CZI file, LSM880).
Processing->Image Alignment->Slice to Slice
The process crashes within 5 seconds every time with an error similar to this one:

Problem signature:

Problem Event Name: CLR20r3

Problem Signature 01: aqiPlatform.exe

Problem Signature 02: 3.1.2.0

Problem Signature 03: 59692193

Problem Signature 04: AutoAlignOperations

Problem Signature 05: 1.0.0.1

Problem Signature 06: 596924ce

Problem Signature 07: 24

Problem Signature 08: cd

Problem Signature 09: System.AccessViolationException

OS Version: 6.1.7601.2.1.0.256.4

Locale ID: 1033

Additional Information 1: 280d

Additional Information 2: 280d17e932c988d6f296e811a53ae5a1

Additional Information 3: 0945

Additional Information 4: 0945bbae75119a17c3551191358bf4b6

Read our privacy statement online:

http://go.microsoft.com/fwlink/?linkid=104288&clcid=0x0409

If the online privacy statement is not available, please read our privacy statement offline:

C:\Windows\system32\en-US\erofflps.txt

----------------
This has happened whether I use recommended settings or attempt to adjust the settings (Black replacement, higher noise thresholds, Severe warping, etc). In the User settings, both temporary files and the default image folder have been set to fully accessible "temp" folders in the base C drive.

Is there anything else I can try, or has anyone run into this problem before? Please let me know if there is any additional information I can provide.

PACS Integration/Export

crobinson — Tue, 19 Sep 2017 20:56:34 +0000

Are there any plans to include an option to export or save directly to PACS systems in the future?

Batch Process in Autoquant

mad8110 — Mon, 17 Jul 2017 15:08:56 +0000

Is it possible to point Autoquant batch processing at a folder instead of having to load the images into the program first? This becomes cumbersome when lots of images stacks are involved.

We need your help to improve our products!

NickB — Tue, 30 Aug 2016 16:05:42 +0000

Deconvolution Software has gone through a recent resurgence due to the implementation of Graphics Processing Unit (GPU) based solutions. To better understand your requirements as a researcher with these new solutions, we request that you complete the attached survey to help us improve the design of our products to better meet your research needs.

https://www.surveymonkey.com/r/6P766WB

Is it possible to perform image alignment before deconvolution using Autoquant connect?

gabi — Mon, 14 Mar 2016 07:18:45 +0000

I am batch processing files and sending them to Autoquant using Autoquant Connect. I would like to specify that Autoquant first performs an alignment of the stacks before performing the deconvolution. Is this possible using the Autoquant Connect file? (I do not manually want to perform an alignment).

Thanks in advance for any advice.

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

gabi — Fri, 18 Sep 2015 09:50:32 +0000

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

Hotfix: Disappearing Dongle ID in Dongle Update utility

AndyM — Mon, 29 Jul 2013 21:24:48 +0000

We have released a hotfix that is intended to address an issue with the AutoQuant X Dongle Update utility in which the "Dongle ID" field appears blank, despite the AutoQuant X dongle being plugged in with its light on.

If you have run into this issue, please try downloading this hotfix, which can be found on our support site here:
http://support.mediacy.com/news/showstory.asp?storyid=121

Open, Export and Save Files in AutoQuant Deconvolution Software - Video Tutorial

NickB — Mon, 17 Jun 2013 17:12:40 +0000

Learn the basic ways to open, export and save files in AutoQuant software.

Watch the video tutorial:
http://www.mediacy.com/index.aspx?page=AQ_vid_open_save

View all AutoQuant video tutorials at:
http://www.mediacy.com/index.aspx?page=Auto_vid_tours

AutoQuant Spherical Aberration Tools - Video Tutorial

NickB — Mon, 17 Jun 2013 17:07:26 +0000

Learn how to improve your image deconvolution using AutoQuant spherical aberration tools.

Watch the video tutorial:
http://www.mediacy.com/index.aspx?page=AQ_vid_spher_ab_tools

View all AutoQuant video tutorials at:
http://www.mediacy.com/index.aspx?page=Auto_vid_tours

Introduction to AutoQuant Deconvolution Software - Video Tutorial

NickB — Mon, 17 Jun 2013 17:03:01 +0000

This video offers an introduction to AutoQuant deconvolution software.

Watch the video tutorial:
http://www.mediacy.com/index.aspx?page=AQ_vid_AutoQuant_introduction

View all AutoQuant video tutorials at:
http://www.mediacy.com/index.aspx?page=Auto_vid_tours

How to Batch Process in AutoQuant Deconvolution Software - Video Tutorial

NickB — Mon, 17 Jun 2013 16:58:56 +0000

Learn how to operate the the batch processing feature of AutoQuant deconvolution software.

Watch the video tutorial:
http://www.mediacy.com/index.aspx?page=AQ_vid_batch_proc

View all AutoQuant video tutorials at:
http://www.mediacy.com/index.aspx?page=Auto_vid_tours

Validating Your Results

AndyM — Tue, 21 May 2013 21:20:52 +0000

A common concern when performing deconvolution arises from the occasional appearance of a structure in a deconvolved result image that did not appear to be present in the raw image. Usually, this is a consequence of the visualization used.

By default, AutoQuant X will display images as maximum intensity projections. While this is a very useful view for getting a quick overview of what's in the stack, it can very easily obfuscate the boundaries between objects. In order to better see those boundaries, we recommend switching to a slice view (View-Slice Viewer). Objects in the raw view that seem much more blurred together in a maximum projection view will typically be easier to visually separate in the slice view.

Try setting both the raw and deconvolved images to the slice view, and then synchronize them, using the chain-link icon at the right end of the image window toolbar (click this in both image windows). Now, altering the scroll bar in one window will update the other to the same position. This allows a simple frame-by-frame visual comparison between the raw and deconvolved stacks that makes it considerably easier to see from where the object boundaries visible in the deconvolved result come.

New AutoQuant X 3.0.2 Released

NickB — Thu, 16 May 2013 13:03:39 +0000

Media Cybernetics announces the release of AutoQuant X 3.0.2 This update is complimentary for all AutoQuant X 3.x users. To upgrade your existing 3.x software, please select "Check for Updates..." from the Help Menu. If you are using AutoQuant X v3.0.0. Please note that this Check for Updates feature requires you to run as an Administrator. Users with AutoQuant X 3.0.1 will not need to run as Administrator to check for updates. Issues addressed in AutoQuant X 3.0.2: General - Addressed numerous exception errors that could appear when operating with one or more channels deselected - Enhanced memory management to resolve numerous exception errors that could occur when loading or processing data - Added "32-bit Version" or "64-bit Version" specifiers to About box File I/O - Improved handling of volumes larger than 2GB in size (esp. LIF and RAW volumes) - Added support for ICS datasets comprised of more than one ICS/IDS file pair (i.e., sequence handling) - Resolved loading errors in ND2 format - Fixed loading of ZVI files with irregular channel indexing - Adjusted output of TIFF datasets to avoid oversized (> 4GB) individual TIFF files - Resolved LZW decompression issue that could cause reads from poorly-compressed data to fail - Added image loading support for Meta ND version 2 files - Corrected numerous meta-data errors - Wavelengths when reading LSM - Spatial calibration when reading ZVI - Lens and sample refractive indices when reading and writing ICS - Microscope modality when writing IMS Deconvolution - Resolved crash when performing spherical aberration detection on large images - Fixed an intermittent crash when processing data on high-RAM (>~32GB) machines - Added multi-threaded processing for 2D blind deconvolution Batch Processing - Added output folder and "Save PSF" settings to copiable operation settings in batch - Improved retention of settings for batched deconvolution tasks when opening tasks for review Colocalization - Corrected calculation of Pearson's and Manders' coefficients - Improved responsiveness of colocalization GUI when operating on large datasets - Fixed a crash that could occur when generating a colocalization image