OpenPolScope MantisBT - Issues

0000087: frame averaging with Flash4 crashes Pol-Acquisition plugin

Mon, 07 Jan 2019 12:12:45 -0500

On Friday, Jan 4, Mai and I used the Nikon inverted stand with the light field camera that now has the new Hamamatsu Flash4 camera with USB connection installed. The Pol-Acquisition plugin in polarized fluorescence mode worked without a hitch, except when we enabled frame averaging. With frame averaging enabled (4 frames), a time series acquisition stalled halfway, and MicroManager needed to be rebooted. Frame averaging seemed to work for some of the acquisitions, but then failed.

Following this experience, we disabled frame averaging (we only recorded sample images, no background was needed), and the rest of the session, taking about 6 hours with many (beautiful) data sets, went flawlessly.

0000086: switching between birefringence and diattenuation processing

Tue, 25 Sep 2018 16:30:47 -0400

Yesterday, a lab visitor (Inigo Novales) brought a sample (anchovy retina) that required switching between birefringence and diattenuation mode for acquisition and reprocessing (Pol-Analyzer) of such image stacks. During this session, we had to restart the ImageJ-MM program several times, because sometimes, when reprocessing a stack, the result did not appear in the specified stack, but was lost, nobody knows where. Only restart remedied the situation. Also, at least once in diattenuation mode, an incorrect background image was used during processing, even though the correct background was specified in the respective entry.

0000085: wavelength change not complete in birefringence mode

Mon, 06 Aug 2018 18:07:41 -0400

After taking retardance images with one wavelength, I changed the wavelength on the scope and entered the new wavelength into the MeadowlarkLC-Controls panel of the Pol-Acquisition window. I then calibrated with the new wavelength, which finished in time, but showed settings for LC-A and LC-B that were quite far off from the usual 0.25 and 0.5. After using the Device Property Browser tool, it calibrated correctly.
My hunch is that the wavelength is initially not set correctly for the first calibration. Might it first use the default value 546nm?

0000084: Remove logging of "BG set to..."

Tue, 10 Apr 2018 16:20:26 -0400

"BG set to..." unnecessarily often in the Log and can be dropped altogether.
It is sufficient that the BG is recorded in the metadata to each image.

0000083: Pol-Analyzer Data Session pull down list seems randomly ordered in session names

Sat, 31 Mar 2018 10:49:06 -0400

Pol-Analyzer Data Session pull down list seems randomly ordered in session names

0000082: swing value logged for diattenuation setting

Fri, 30 Mar 2018 16:54:59 -0400

A swing value is logged when diattenuation setting is enabled.
There is no swing value for diattenuation

0000081: Pol-Analysis,"Use ROI from Sample Metadata from Background" toggles on/off indefinitely

Mon, 26 Mar 2018 16:08:57 -0400

In Pol-Analysis, after opening BG stack, "Use ROI from Sample Metadata from Background" toggles on/off indefinitely

0000080: Acquired Diatt. Stack shows only 6 out of 7 slices

Mon, 26 Mar 2018 15:17:24 -0400

The data set is saved correctly, but incompletely displayed after acquisition.
Loading the data set with Pol-Analyzer displays all slices

0000079: Pol-Analyzer, new Logger text not loaded, etc.

Sun, 12 Mar 2017 17:30:18 -0400

1. New Logger text not loaded (visible) after switching to new session.

This seems to happen only after at least one polstack was opened.

When testing it without opening a polstack after restart, the Logger text will show fine.

Once the Logger text doesn't show, only quitting MM and restarting it will make the Logger text reappear.

2. When starting MM and then Pol-Analyzer plugin, the default session is not the session that was active before last quit, unless the Pol-Analyzer plugin was closed and reopened during the last session.

3. Sometimes the "Editable Info" in session.polSession is inappropriately overwritten. Also, it seems that this info in the Mac version of Pol-Analyzer plugin is added to the end of the session.polSession file, while the Windows version puts it at the beginning of the file.

0000078: ratio value decimal readout

Sat, 09 Apr 2016 11:16:42 -0400

Increase decimals in displayed/printed ratio values from 1 to 3.

For example, display ratio value 1.123 instead of 1.1

0000077: orientation cursor for z-stack

Mon, 12 Oct 2015 15:16:34 -0400

orientation cursor for z-stack not reading correct azimuth values
possibly only for first z-slice correct

0000076: In diattenuation mode image path mirror setting inactive

Mon, 28 Sep 2015 16:50:05 -0400

Make image path mirror setting active

0000075: MO device delay inactive by default

Wed, 23 Sep 2015 18:54:40 -0400

MO device delay inactive by default, becomes active after entering delay in Property Browser, observed in Diattenuation mode.

0000074: Keep shutter open during pol acquisition sequence

Wed, 23 Sep 2015 16:31:53 -0400

Keep shutter open during pol acquisition sequence and calibration

0000073: remove aBg and bBg from Polarized Fluorescence tab

Fri, 04 Sep 2015 16:32:08 -0400

remove aBg and bBg from bottom of Polarized Fluorescence tab

0000072: Dialog for opening MMPolStack always starts inside first SM... folder

Fri, 04 Sep 2015 15:39:17 -0400

Dialog should start with session folder.

0000071: Birefringence acquisition: LC settings not recorded in metadata of raw images

Mon, 24 Aug 2015 14:19:03 -0400

In the metadata of the raw images, the palette elements are empty and the Retardance LC-A and LC-B show what I think are the values for the extinction setting for all elliptical settings as well.

0000070: Error on first reprocess of Pol-fluorescence images

Sun, 23 Aug 2015 21:56:00 -0400

After clicking Process, error message "Images with more than 7 channels cannot be displayed in Composite mode".

After clicking OK on this error message, reprocessing the same image completes correctly, without error message.

Opening a new polstack and processing it will again trigger the error message, while the second processing will again complete correctly.

0000069: First acquisition stalls

Sun, 23 Aug 2015 15:12:50 -0400

After starting ImageJ/MM/Pol-Acquisition the first time, the first pol-acquisition using either BG or SM stalls, never completes and prevents closing of ImageJ/MM. However, the Pol-Acquistion window can be closed.

After ending javaw.exe process and restarting ImageJ/MM/Pol-Acquisition, all further acquisition requests execute correctly.

0000068: Change Fluorescence Polarization to Polarized Fluorescence

Sun, 23 Aug 2015 14:45:54 -0400

In OPS environment, change all occurrences of Fluorescence Polarization to Polarized Fluorescence

0000065: Micro-Manager errors

Tue, 24 Dec 2013 20:39:48 -0500

When I opened Micro-Manager I saw this massage below:

"Line 16: Property,MeadowlarkLC,Number of Active LCs,2
Error in device MeadowlarkLC: Invalid property name encountered: Number of Active LCs. (Error code: 2)

Line 17: Property,MeadowlarkLC,Select Device #,1
Error in device MeadowlarkLC: Invalid property value: Select Device #. (Error code: 3)

Line 18: Property,MeadowlarkLC,Select Device Type,20V (D3060HV) Controller
Error in device MeadowlarkLC: Invalid property name encountered: Select Device Type. (Error code: 2)

Line 19: Property,MeadowlarkLC,Serial/Version No.,123
Error in device MeadowlarkLC: Invalid property name encountered: Serial/Version No.. (Error code: 2)

Line 20: Property,MeadowlarkLC,Total Number of LCs,4
Error in device MeadowlarkLC: Invalid property name encountered: Total Number of LCs. (Error code: 2)

Line 21: Property,MeadowlarkLC,Total Number of Palette Elements,5
Error in device MeadowlarkLC: Invalid property name encountered: Total Number of Palette Elements. (Error code: 2)

Line 30: Property,Core,Initialize,1
Error in device MeadowlarkLC: Unable to communicate with the device..

Line 37: Property,Core,Camera,Hamamatsu_DCAM
Attempted to set "Core-Camera" to "Hamamatsu_DCAM".
Core property is read-only or the requested value is not allowed.

Line 38: Property,Core,Focus,TIZDrive
Attempted to set "Core-Focus" to "TIZDrive".
Core property is read-only or the requested value is not allowed."

However it seems there are some problems with my computer as well. It doesn't see the usb so it might not see the LCs. Otherwise I don't know.

0000034: List of actions that report to Logger panel

Thu, 19 Sep 2013 15:33:00 -0400

List of actions that report to Logger panel:

Currently implemented.
1. Acquiring SM, BG, Series with comment
2. Creating new user, session
3. Changing Mode Plugin
4. Acquiring non Pol image via Album button
5. Calibrating Diattenuation, FluorPol (Anisotropy, Orientation)

To implement.

Recently Implemented.
1. Implement in Pol-Analyzer
2. Birefringence calibration

0000058: Enable interupt when drawing orientation lines

Wed, 18 Sep 2013 15:00:07 -0400

When drawing orientation lines is set to every pixel (interval=1), it can take a long time (~30 sec)for the lines to show when image is large (2,000x2,000.

Enable to cancel the lines by removing (unclicking) the checkmark

0000063: Create default settings using current swing setting

Mon, 16 Sep 2013 17:58:17 -0400

I suggest to create the default settings using the current swing value

0000062: Pol-Analyzer, draws orientation lines even if not selected

Mon, 16 Sep 2013 08:55:20 -0400

When reprocessing a sample image, orientation lines were drawn, even if not selected.