87 OpenPolScope-API rudolfo amit high major always assigned open none bug 1546881165 1546881165 none Windows Nikon inverted, Ham Flash4 public

frame averaging with Flash4 crashes Pol-Acquisition plugin

1 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. 86 OpenPolScope-API rudolfo amit normal major sometimes assigned open none bug 1537907447 1537907447 none Windows 7 Nikon inverted station public

switching between birefringence and diattenuation processing

1 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. 85 OpenPolScope-API rudolfo amit high major always assigned open none bug 1533593090 1533593261 none Nikon Ti station public

wavelength change not complete in birefringence mode

1 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? 84 OpenPolScope-API rudolfo normal minor always new open none enhancement 1523391626 1523391626 none All All public

Remove logging of "BG set to..."

1 "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. 83 OpenPolScope-API rudolfo normal minor always new open none bug 1522507746 1522507746 none OSX Macintosh public

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

1 Pol-Analyzer Data Session pull down list seems randomly ordered in session names 82 OpenPolScope-API rudolfo normal minor always new open none bug 1522443299 1522443299 none Windows Ti-E workstation public

swing value logged for diattenuation setting

1 A swing value is logged when diattenuation setting is enabled. There is no swing value for diattenuation 81 OpenPolScope-API rudolfo normal major always new open none bug 1522094937 1522094937 none Windows 10 Workstation at Nikon Ti-E Inv. public

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

1 In Pol-Analysis, after opening BG stack, "Use ROI from Sample Metadata from Background" toggles on/off indefinitely 80 OpenPolScope-API rudolfo amit normal major always assigned open none bug 1522091844 1522091844 none Windows 10 Workstation at Nikon Ti-E Inv. public

Acquired Diatt. Stack shows only 6 out of 7 slices

1 The data set is saved correctly, but incompletely displayed after acquisition. Loading the data set with Pol-Analyzer displays all slices 79 Birefringence rudolfo amit normal minor always assigned open none bug 1489354218 1489354218 none MacOS 10.12.3 2.2 public

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

1 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. 78 Diattenuation rudolfo amit normal minor always assigned open none enhancement 1460215002 1460215002 none All public

ratio value decimal readout

1 Increase decimals in displayed/printed ratio values from 1 to 3. For example, display ratio value 1.123 instead of 1.1 77 Pol-Acquisition rudolfo normal major always new open none bug 1444677394 1444677394 none public

orientation cursor for z-stack

1 orientation cursor for z-stack not reading correct azimuth values possibly only for first z-slice correct 76 Pol-Acquisition rudolfo amit normal minor always assigned open none bug 1443473405 1443473405 none public

In diattenuation mode image path mirror setting inactive

1 Make image path mirror setting active 75 Pol-Acquisition rudolfo amit high major always assigned open none bug 1443048880 1443048880 none public

MO device delay inactive by default

1 MO device delay inactive by default, becomes active after entering delay in Property Browser, observed in Diattenuation mode. 74 Pol-Acquisition rudolfo amit normal major always assigned open none bug 1443039881 1443040313 none public

Keep shutter open during pol acquisition sequence

1 Keep shutter open during pol acquisition sequence and calibration 73 Pol-Analyzer rudolfo amit normal minor always assigned open none bug 1441398728 1441398728 none public

remove aBg and bBg from Polarized Fluorescence tab

1 remove aBg and bBg from bottom of Polarized Fluorescence tab 72 Pol-Analyzer rudolfo amit normal minor always assigned open none bug 1441395557 1441395557 none public

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

1 Dialog should start with session folder. 71 MeadowlarkLC rudolfo amit high major have not tried assigned open none bug 1440440343 1440440343 none public

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

1 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. 70 Fluorescence Polarization rudolfo amit high minor always assigned open none bug 1440366859 1440381360 none Pol-Analyzer public

Error on first reprocess of Pol-fluorescence images

1 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. 69 Fluorescence Polarization rudolfo amit high crash always assigned open none micro-manager bug 1440357170 1440357170 none Nikon inverted/Flash4/MLO-LCs public

First acquisition stalls

1 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. 68 Fluorescence Polarization rudolfo amit normal minor have not tried assigned open none General 1440355554 1440355554 none public

Change Fluorescence Polarization to Polarized Fluorescence

1 In OPS environment, change all occurrences of Fluorescence Polarization to Polarized Fluorescence 65 MeadowlarkLC Mai Tran amit normal minor sometimes resolved no change required none micro-manager bug 1387904413 1387935588 none public

Micro-Manager errors

1 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. 34 Pol-Acquisition amit normal minor have not tried new open none enhancement 1372835118 1379619180 none 2.1 2.2 public

List of actions that report to Logger panel

1 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 58 Pol-Acquisition rudolfo amit normal minor always feedback reopened none bug 1379271547 1379530807 none Windows 7 2.17 2.17 public

Enable interupt when drawing orientation lines

1 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 63 Pol-Acquisition rudolfo amit normal minor N/A assigned open none feature-request 1379368697 1379368697 none Windows 7 2.17 public

Create default settings using current swing setting

1 I suggest to create the default settings using the current swing value 62 Pol-Acquisition rudolfo amit normal minor always assigned open none bug 1379272401 1379336120 none Windows 7 2.17 public

Pol-Analyzer, draws orientation lines even if not selected

1 When reprocessing a sample image, orientation lines were drawn, even if not selected. 60 Pol-Acquisition rudolfo amit normal minor always assigned open none bug 1379272191 1379272191 none Windows 7 2.17 public

List of window titles in ImageJ>Windows is mixed up

1 MM stacks in ImageJ>Windows menu are incorrectly named. 25 OpenPolScope-API admin normal minor have not tried new open none enhancement 1372555745 1376172143 none 2.15 2.18 public

Show Invalid Pixels

1 Use an overlay to color (say red) any pixels in a computed image where the the value of this pixel in any of the sample images is saturated. 55 OpenPolScope-API amit amit normal minor have not tried assigned open none enhancement 1376169919 1376172078 none 2.16 2.17 public

sub-plugins should work with stack option disabled in Pol-Analyzer Options

1 Sub-plugins (eg. ColorMap) should work with stack option disabled in Pol-Analyzer Options. This is useful to export a selected timepoint/z-plane without reprocessing the complete stack and then exporting the required image. 32 OpenPolScope-API shalin normal minor have not tried new open none feature-request 1372812012 1376171855 none 2.15 2.2 public

Enable calling Pol-Analyzer's data-conversion functions from MATLAB

1 It will be efficient if users can transparently get data computed by MATLAB converted into format compatible with Pol-analyzer. My prefeered workflow would be like this (using Fiji): >Miji(false); >MIJ.Run('Pol-AnalyzerDataConverter','PathtoTifffile.tif'); It is OK to overwrite the tif file Pol-Analyzer format data. 52 Orientation Lines V4 admin grant urgent feature have not tried assigned open none enhancement 1375483386 1375483449 none 2.15 2.16 public

glyphs / circular statistics for Orientation lines

1 add glyphs / circular statistics / additions from Grant/Rudolf/Hannah's code Added by Shalin: We have been using Pol-Analyzer for exploring data taken in collaboration with Clare Waterman's group (mostly real-time PolScope data converted to MM format) and with Daniel Gerlich (Nikon PolScope). In both cases, we need to compare average anisotropy/orientation in following ways: a) When the lines are plotted every Nth pixel, it is expected that intensity is averaged over NXN pixels before the anisotropy/orientation are calculated and plotted. We can plot the orientation line at the center of NXN pixels. b) Often times the biologically interesting measurement is to compare net anisotropy over manually selected regions. We would like to draw a ROI manually and obtain anisotropy/orientation using intensities averaged over that ROI. c) An extension of b) for rectangular ROI is that the ROI can be partitioned into rows and columns with anisotropy/orientation obtained over each sub-ROI (the mode that Rudolf implemented with ROI averages with Lines V1). For b) and c) an option to plot orientation fan (displaying average orientation and its variance as Grant has implemented) will be quite informative. It seems that a) is properly implemented within current Azim Lines plugin as an option. It seems that b) and c) can be made by combining Rudolf's plugin and Grant's orientation fan. If we can bump these feature requests higher in priority, they can receive good use and testing over next few weeks. Also, it is important to be able to export the values, for example by pushing them to the measurement window of ImageJ. moved from Orientation Lines V3 project (Issue #24) 26 Diattenuation admin normal minor have not tried new open none enhancement 1372555836 1375482613 none 2.1 2.2 public

UI for Calibration Process

1 Not evident that one can EITHER use 'Single ROI Calibration' or 'Four ROI calibration' method. Perhaps have a radio button to choose one or the other, and enable the panel for the chosen method.