odemis (3.0.0-1) xenial; urgency=medium * New version: 3.0 * Main new features: - Support for Python 3. Python 2.7 is still supported, but deprecated. - Support for Ubuntu 18.04 - Ruler tool the GUI, to measure distance on the images - SPARC acquisition streams now support arbitrarily long exposure time * Main improvements and bug fixes: - Hardware can be automatically turned off when the back-end is stopped - Log format has been adjusted to be more readable & parsable - Background correction also available for temporal spectrum data - Fix raw export of data with float types or large ints - When opening data with both AR and spectrum, a dialog box proposes to select which one to show - odemis-cli --live on a detector with a single pixel shows the value of the pixel - UEye camera driver supports 12- and 16-bit depth - Timelapse plugin has a "fast-mode" when the period is small and only one stream is acquired - Automatic reconnection to the TMCM, PMT control unit, and Andor spectrograph. * Improvements and bug fixes already present in v2.10 branch: - When exporting a Fluorescent stream (or a RGB CL stream) the legend didn't contain any information - Never try to move the focus of the Andor SR303, because it doesn't have a focus - In some cases the tile plugin could incorrectly warn on that the computer doesn't have enough memory - Cancelling an acquisition in the RGB CL plugin actually didn't stop the acquisition - bugreporter: Don't fail if description.txt contains non-ascii characters - Don't fail to show acquisition file if the language settings lead to a date containing non-ascii characters - Fix knob connection (DELPHI) - Fix polarization metadata failing to load in some (rare) cases - Don't move Labcube filters at startup if they are already referenced - Small tweaks to the spectrum zoom/drag functionality in the GUI - Time-resolved live view chronograms were limited to the first 1024 points - Don't limit chronograms to the first 1024 points - Fix piconfig & pituner utilities - Sometimes the back-end would block when terminating - andorcam2 CCD can have targetTemperature = 25°C to indicate the cooler should be disabled - Show EM CCD gain setting on SPARC if the camera supports it - Force to use wxPython 4.0 on Ubuntu - Zeiss: detect if connected to the wrong device -- Éric Piel (Delmic) Thu, 07 Nov 2019 11:01:13 +0100 odemis (2.10.0-1) xenial; urgency=medium * New version: 2.10 * Main new features: - Support for time-resolved acquisition (SPARC) - Support for temporal-spectrum acquisition (SPARC) - Can visualize polarized angle-resolved as Stokes parameters and degree of polarization - Possibility to zoom in/out the spectrum and time plots - Plugin to remove spikes from spectrum data (SPARC) - Plugin to acquire large-area spectra (SPARC) * Main improvements and bug fixes: - Support for SPARCs with 4 spectrometers - Warn if SECOM fine alignment measures unexpected magnification - Tile acquisition plugin can run fine alignment after each tile (SECOM/DELPHI) - GUI doesn't freeze when starting autofocus (SPARC) - SPARC autofocus waits for the calibration light to turn on before starting - Allow to change the tint of the StaticCLStream - Support for IDS uEye GigE camera - Support for PI E709 actuator controllers - Support for Andor Kymera 328 - Support for Hamamatsu Streakcam - Support for wheel-based Optical Density filters - Extended support for PicoQuant PicoHarp300 - SECOM CL plugin accepts ROA, drift correction and non-square pixels. - Support for TMCM axes controlled via digital output - TMCM axes referenced are detected even after a back-end restart - Microscope files now distinguish between "children" components and "dependency" components - GUI doesn't show peak fitting warnings as errors - Option to wait for blanker/external signal stability in SEM external scan - Can display image from Catmaid server - Debian package also works on Ubuntu 18.04 - More information about the system is sent in bug reports * Improvements and bug fixes already present in v2.9 branch: - Fix Windows Viewer not building with wxPython4 - Persistent metadata could be overridden by default metadata - Fix referencing on TMCM sometimes timing out too early - Andor shamrock with a mirror "grating" only really accepts center wavelength 0 - Previous HDF5 time-correlator acquisitions were not read back properly - In some cases, the microscope file could be missing from the bug report - On an acquisition with a Z stack, going to Z=0 via the Z index didn't have any effect - In the GUI, if an axis move (eg, wavelength) was rejected by the hardware, it would be shown as if it succeeded. - AR export to CSV was mirrored on the phi axis - Large AR projections with background failed - Polarized AR export to CSV would not always correspond to the selected polarization - Display of AR polarized images would sometimes not appear for some polarizations - Andor Shamrock could report a communication issue if the CCD settings were changed while changing the grating - Fix rare case where GUI could crash during SECOM/DELPHI acquisition - Don't raise an error when changing CCD fan speed fails (SECOM) - Changing the Fluorescence stream tint didn't always work (SECOM) - OmicronxX could miss some answer from the hardware (SECOM) - MultiplexActuator didn't report the very first position change - plugin cli-rgb failed to estimate the acquisition time if drift correction was selected -- Éric Piel (Delmic) Thu, 18 Jul 2019 09:57:24 +0200 odemis (2.9.0-1) precise; urgency=medium * New version: 2.9 * Main new features: - Support for polarizer acquisition (SPARC) - Support for FLIM acquisition (SECOM confocal) - Option to see the metadata of the streams in the analysis tab - New bug reporter, which can directly upload the reports - Plugin to acquire Z-stack - Ability to vizualise Z-stack data - Support for Trinamic TMCM-3214 actuator - Support for Newport ESP301 actuator * Main improvements and bugs fixes: - Migrated to wxPython 4 - More reliable stitching register based on global optimisation - New stiching weaver "CollageReverse" which prefers the first image acquired - Focus position of spectrometer was not properly remembered if the main detector was on the second port (SPARC) - In the GUI, on arrow key, move 10% of HFW, instead of always 100px - Fix updater and make it download faster (Viewer on Windows) - New util grupdate: to extract and merge log - New util axes-odometer: to measure the traveled distance based on the log - New util piterminal: to connect directly to a PI controller - When opening large data in pyramidal format, sometimes no image would be shown - Do software binning if spectrometer CCD doesn't support full vertical binning (SPARC) - Backend can restore properties and metadata at init (ie, persitent settings) - Extented and clarified developer documentation * Improvements and bug fixes already present in v2.8 branch: - Fix live SPARC AR view not always centered if stage can be controlled - Ensure the ebeam is positionned properly before acquiring a CCD image (SPARC) - AR pole position was not immediately updated after the alignment (SPARC) - Fix reading extra parameters of the TMCM in some cases (SPARC) - On the first load after starting odemis, the optical focus wasn't set (DELPHI) - ConvertStage wrapping a stage with canUpdate would fail if using the canUpdate feature - On Windows, the new libtiff couldn't be loaded - Tescan driver supports .external and .blanker (only manual) - Tescan driver doesn't require a stage - odemis-cli --position accepts negative floats and string as positions - Way to override the order of the axes during SPARCv2 mirror parking: AXES_ORDER_REF - Fix file association for OME-TIFF on Linux - PI controllers in closed-loop could have large unexpected movements if not moved for a long time - Tile acquisition plugin was overly optimistic on memory usage on the SECOM/DELPHI - Windows viewer didn't build properly - Fix metadata update from component with None role (DELPHI) - Clarify some log messages - plugin quickcl: support also monochromator - ConvertStage could cause large unexpected move if requested absolute move with only one axis - A monochromator placed on an external spectrograph could miss some metadata - plugin quickcl: failed to show window - plugin tileacq: failure during acquisition was not displayed * Deprecation notes: - This is the last version supporting Ubuntu 12.04 -> upgrade to Ubuntu 16.04 - This is the last version supporting wxPython 3 -> upgrade to wxPython 4 -- Éric Piel (Delmic) Wed, 28 Nov 2018 11:02:37 +0100 odemis (2.8.0-1) precise; urgency=medium * New version: 2.8 * Main new features: - GUI detects filename pattern entered by user and follows it - Option to insert streams from a second acquisition file in the Analysis tab - Tile plugin will show a warning if attempting to acquire too many tiles given the computer memory available - Background subtraction available in SPARC mirror alignment - Support for Rigol DG1000z as clock generator - Support for synchronisation with PicoQuant SymPhoTime * Main bugs fixed: - Spectrum and chronogram plot rounded too much the values displayed - Tile acquisition doesn't require anymore a lot of memory when stitching is disabled - After exporting a spectrum, the spectrum plot would not display correctly the legend anymore - Tileacq and Timelapse plugins now handle properly any stream of the SPARC * Improvements and bug fixes already present in v2.7 branch: - Support for Zeiss SEM contron via the Remcon interface - Support for software interlock between andorshrk and external component - Timelapse plugin has option to acquire the SEM image only once, at the end - When doing large moves, don't show every intermediary position in the overview image (SECOM/DELPHI) - plugin tile-acq wouldn't accept to store filenames containing "%" - stitching would too easily fail on the tiles on the back zigzag line - ensure the lens1 is always in place for acquisition (SPARC) - fix (rare) GUI crash when a plugin would display an acquisition in the analysis tab - Exporting pyramidal TIFF image didn't use the right field-of-view - Windows version would try to write libtiff header file in directory without permissions - Windows version would fail to start if username contained non-ascii characters - Stage movement of Zeiss SEM always failing if axes are inverted - Ensure the backend log file is rotated as soon as it's > 100Mb - Tile plugin would try to open stiched file, even if no stitching was performed - Associate Odemis Viewer to TIFF and HDF5 files in Windows too - Show PicoHarp SyncDivider option in the time-correlator plugin - Support saving pyramidal image in Serialized TIFF too - Add SyncDivider control to the picoquant driver - Display spectrometer camera in SPARC alignment if no calibration camera - Avoid closed-loop axes staying locked on the physical limits (SECOM) - Handle renamed Serialized TIFF with multiple streams - Don't move the chamber view based on the stage position (SPARC) - Store snapshot of spectrum with correct metadata (SPARC) - Store the output of cliccd as a float, to avoid quantisation (SPARC) -- Éric Piel (Delmic) Mon, 14 May 2018 12:55:21 +0200 odemis (2.7.0-1) precise; urgency=medium * New version: 2.7 * Main new features: - Support for stitching image tiles into a large image - Support for saving pyramidal TIFF images - Support for displaying pyramidal TIFF images - Overview image builds up while moving around the sample (DELPHI/SECOM) - "Tile acquisition" plugin to acquire large scale images - "CCD-as-a-CL-detector" plugin (SPARC) - "Add image" plugin to insert an acquisition into another acquisition - "Automatic alignment" plugin to add an extra EM image to a CLEM acquisition - "CL time-correlator acquisition" plugin (SPARC) - "AR/Spectral" plugin (SPARC) - Support for probe current detector during SPARC acquisition - Support of the Keithley 6485 microammeter * Behaviour change: - Plugins are now loaded from /usr/lib/odemis/plugins, instead of /usr/share * Main improvements: - Improve reliability of Phenom driver (DELPHI) - Additional low-level control of Andor iXon and Newton CCDs (SPARC/SECOM) - Support for manually changing the turret on Andor Shamrock (SPARC) - Simplification of the mirror alignment tab (SPARC) - Support for confocal fluorescence microscope (instead of CCD) with the SECOM - Support for SPARCv2 mirror stage on SPARCv1 microscopes - Improve reliability of the IDS USB camera (SPARC compact) - The back-end detects more types of errors in the microscope file * Main bugs fixed: - Turn off the emission status led when no emission is active on omicron ledhub (DELPHI/SECOM) - Stream could sometimes be playing in background if acquisition is cancelled early (SPARC) - When a dye has no emission wavelength fitting, pick the closest one anyway (DELPHI/SECOM) - When centre wavelength is at 0, show it as "0 nm" instead of "0 m" (SPARC) - Allow to enter "None" on odemis-cli in addition to "null" - Allow typing "µ" into number field (for unit prefix) -- Éric Piel (Delmic) Tue, 16 Jan 2018 13:11:40 +0200 odemis (2.6.0-1ubuntu1) precise; urgency=medium * New version: 2.6 * Main new features: - pwrcomedi driver to control device power via any DAQ board - cobolt driver to control Cobolt laser power - MultiplexLight wrapper to merge multiple light devices into a single component - "CL acquisition" plugin to acquire CL data on a SECOM/DELPHI - "Averaged frame" plugin to acquire SEM images via fast accumulated scans - Optical focus is restored to a "good" value when inserting a sample (DELPHI) - Use a separate focus in chamber view from the acquisition focus (SPARCv2) * Main improvements: - Do not restart live stream when coming back to the acquisition tab - Improved reliability of the DELPHI calibration - Store logs and attach them to bug report in case of failure of the DELPHI calibration - Updated tooltip information for each acquistion setting - Fuzzing acquisition use always the finest e-beam resolution possible (SPARC) - CCD temperature display in SPARCv2 alignment tab - Possibility to zoom & pan in SPARCv2 lens alignment - Fiber alignment chronograph scales to data range (SPARC) - Only provide a text entry to change the spectrometer center wavelength (SPARC) - Better logging in case of failure or errors * Main bug fixed: - Prevents sample to be moved outside of the physical limits of the axes (DELPHI) - Workaround power control unit sometimes diconnecting when turning on the power (SPARC) - Ensure the SEM HFW is never modified when the GUI window is resized * Bugs fixed also in the stable v2.5 branch: - Don't try setting extremely long exposure times in high-quality presets (DELPHI/SECOM) - Zooming a lot on 1x1 px image could fail - Editing the microscope file would fail when using a MODEL_SELECTOR (SPARC) - CCD fan would not automatically stop during high-quality acquisition (DELPHI/SECOM) - When exporting just one stream, use the stream name instead of the view name - HFW values were not ordered (DELPHI) - First image acquired from Phenom could be showing old data (DELPHI) - In case of automatic calibration failure, it was impossible not to run the manual calibration (DELPHI) - Bandwidth reported by omicronxx driver was 2x bigger than when opening back an image (DELPHI/SECOM) - Limit stage positions during Twin stage calibration to improve reliability (DELPHI) - Fix reduced precision when SEM dwell time > 12s (SPARC) - Fix editing the microscope file and odemis.conf failing to show the editor - Try to handle better acquisition errors of uEye cameras (SPARC) - Reuse name of current file and store current path for export file names - Show the date of the file as the data of the _latest_ acquisition - Show the tint of the filtered stream in legend of print-ready export (SECOM/DELPHI) - Increase font size of spectra and AR print-ready exports (SPARC) - Fix post-processable spatial export of spectra (SPARC) - Fix export of spectra with pixel width > 1 (SPARC) - Fix post-processable line-spectrum export (SPARC) - Fix SEM stream doing twice alignement during high-quality acquisition (DELPHI) - Fix shutter handling on SR193 (SPARC) - Avoid potential GUI crashes when sample holder loading is completed (DELPHI) - Don't attempt to autofocus CCDs with 1D (SPARC) - Don't hide streams automatically on stage move (SECOM) - Change Picoharp driver to provide pixelDuration VA instead of binning (SPARC) -- Éric Piel (Delmic) Thu, 05 Jan 2017 10:46:05 +0100 odemis (2.5.0-1ubuntu1) precise; urgency=medium * New version: 2.5 * Main new features: - Report in the GUI when the SEM stream is being aligned, and when it's not aligned (DELPHI) - Report in the GUI when the hardware is moving to change the optical path (SPARC) - Export line spectra to PNG, TIFF or CSV (SPARC) - Add support for Picoquant PicoHarp time-correlator - Add support for IDS uEye USB cameras - Support for SPARCcompact, which doesn't have an AR camera - Support for shutter on spectrograph with multiple cameras * Main improvements and bugs fixed: - Reduce memory usage - Handle Andor Zyla deconnection/reconnection - Do not show streams which are known to be mis-aligned (DELPHI) - Include calibration and fine alignment logs in bug report (DELPHI) - Fix view in SECOM/DELPHI acquisition sometimes having a very large HFW - Improve DELPHI calibration robustness - Autofocusing the spectrograph, does so for each grating (SPARC) - Avoid warnings about wrong wavelength in GUI when wavelength is near 0nm (SPARC) * Improvements also present in stable v2.4 branch: - Windows updater knows about the new website URL - Fix (disabled) post-processing export of 16 bits data with interpolation - Don't try to load the sample if the door is closed without sample (DELPHI) - Fix some (rare) GUI crashes after autofocus (SECOM/DELPHI) - Only use Phenom high-refresh rate with very latest Phenom v4.4.2+ (DELPHI) - Better rotation correction when doing fine alignment on DELPHI - Very long CCD acquisitions (>60s) could sometimes fail (SPARC) - Andor spectographs with two detectors configured could be set in wrong offset (SPARC) - Optical path could be incorrect if the optical stream wasn't played live before acquisition (SPARC) - Changing spectrum stream bandwidth manually caused it to become 0 (SPARC) -- Éric Piel (Delmic) Mon, 12 Sep 2016 16:17:50 +0200 odemis (2.4-1ubuntu1) precise; urgency=low * New version: 2.4 * Main new features: - Export images for spatial view to PNG or TIFF - Export spectra view to PNG, TIFF, or CSV (SPARC) - Export angular-resolved view to PNT or TIFF (SPARC) - GUI plugin framework for easy extention of the GUI in Python - Plugin for acquiring a spectrum using a monochromator and scanning the center wavelength (SPARC) - Plugin for repeatedly acquiring a stream at a given frequency (SECOM/DELPHI) - Option to display image with interpolation * Main improvements and bugs fixed: - Avoid unexpected small stage move after end of move on PI controllers (SECOM) - Reduced latency in manual optical focus (SECOM/DELPHI) - Speed up auto-focus - Improve default SEM focus on DELPHI - Higher SEM framerate on DELPHI - Fix sporadic SEM tilt issues on DELPHI - Allow non 1:1 image ratio in SEM scanning with semcomedi driver - Support for backlight with Blinkstick (SECOM) - Fix memory leak when opening acquisition file - New 'pituner' utility program to tune PID values of PI controllers - Fix exposureTime shared for all optical stream in acquisition window (SECOM/DELPHI) - Don't change fine alignment dwell time when exposure time of filtered stream is changed (SECOM) - Show a warning if trying to calibrate a sample holder of wrong type (DELPHI) -- Éric Piel (Delmic) Tue, 19 Apr 2016 14:47:44 +0200 odemis (2.3-1ubuntu1) precise; urgency=low * New version: 2.3 * Main new features: - Support for SPARCv2 - Handle power supplier components in backend - Support for Phenom knob (Griffin Powermate) to change focus (DELPHI) - Peak detection in point spectrum analysis (SPARC) - Option to force sample holder recalibration (DELPHI) - Support for Tescan SEM * Main improvements and bugs fixed: - Support for unit prefix when entering values in GUIs - Allow to select filter in spectrum stream (SPARC) - Automatically selects the whole ROI on new CLi stream (SPARC) - Improve manual sample holder calibration interface (DELPHI) - Autofocus speed and quality improvement - Add button to close/open GUI log panel - Fix no update of progress bar during SPARC acquisition - Improve connection between view HFW and SEM HFW (DELPHI) - Allow to start Odemis viewer with a file to open - Allow to indicate a move on the CLI by its position name - Tools to read/write configuration of PI and TMCM controllers - Support for Andor Zyla in spectrum mode (SPARC) - Support for multiple TMCM, Andor2 cameras, and Andor shamrocks - Support for EBIC detector input - Add 'transp' argument to CCD components to replace broken 'transpose' argument -- Éric Piel (Delmic) Tue, 02 Feb 2016 10:19:48 +0100 odemis (2.2-1ubuntu1) precise; urgency=low * New version: 2.2 * Main new features: - SPARC acquisition tab now can show live view of all the streams - Alignment tab can display chamber view (SPARC) - Local settings of light power and exposure time on optical streams (SECOM/DELPHI) - Partial support on Windows: GUI in viewer mode - Spot mode tool in acquisition tab (SPARC) - Support for analog PMT acquisition (SPARC) - Support for counting PMT acquisiton (SPARC) - Support 'fuzzing' on spectrum stream to avoid aliasing (SPARC) - Option to save TIFF files as one file per stream - Support for blinkstick (for bright led, on SECOM) * Main bugs fixed and improvements: - Bug report functionality in GUI menu and Ubuntu icon - In analysis tab, automatically shorten histogram width - Support for parabolic mirrors of various sizes (SPARC) - Allow to acquire multiple streams per acquisition (SPARC) - Improve alignment optical/sem stage (DELPHI) - SEM focus step size depends on HFW (DELPHI) - Ensure the Phenom unblanking always works and tilt value is correct (DELPHI) - New (different) icon for Odemis viewer - Small tools for maintenance/testing - Support for Omicron LedHub (SECOMv2) - Support for Andor Shamrock connected over USB (SPARC) - Support inversing contrast on semcomedi - Skew correction is also applied in the SECOM - In some cases two optical stream could play simultaneously (SECOM) - Don't save all the anchor regions, because that could take too much memory (SPARC) -- Éric Piel (Delmic) Thu, 27 Aug 2015 15:49:20 +0200 odemis (2.1-1ubuntu1) precise; urgency=low * New version: 2.1 * Main new features: - Correct for the shear and X/Y ratio scanning inaccurcies (DELPHI) - Progress bar when (un)loading the sample (DELPHI) - Support for New Focus Picomotor controllers 8742 - Automatically turn off encoders for PI closed-loop, to reduce stage drift. (SECOM) - Button to run the hardware auto contrast (DELPHI) * Main bugs fixed and improvements - SEM view is always centered (DELPHI) - Improved SEM/Optical alignment (DELPHI) - Better looking warning message if the SEM/Optical alignment failed (DELPHI) - Hardware settings are ordered is some logical way - Manually changing the brightness/contrast on a 8-bit image works - During acquisition with drift correction, if the ROI goes out of bound, the acquisition is not automatically discarded. (SPARC) - Absolute move on inversed axis goes to the right place - Allow to override the maximum scanning size on the semcomedi - Do not provide bright-field stream if the hardware doesn't allow this (SECOM/DELPHI) -- Éric Piel (Delmic) Wed, 25 Feb 2015 16:46:27 +0100 odemis (2.0-1ubuntu1) precise; urgency=low * New vesrion: 2.0 * Main new features: - Dynamic backend allows to start with not all hardware turned on and provide user feedback - New line tool to cross-cut spectrum cube into a space/wavelength projection (SPARC) - Width selection for the point and line spectrum tool (SPARC) - Gallery/Analysis tab automatically adapts to the file type displayed - Support for X/Y objective stage (SECOMv2) - DELPHI sample holder calibration can be done via the GUI * Main bugs fixed and improvements - Drift correction was moving incorrectly (SPARC) - Anchor region acquisitions are now saved in the acquisition file (SPARC) - Possibility to select the drift correction period (SPARC) - Beam shift is used to align the SEM on the optical image (DELPHI) - Autofocus was sometimes using the second best position (DELPHI) - Much more precise and robust calibration for the DELPHI - Improve reliability of the connection with the Phenom (DELPHI) - Many small improvements/simplifications in the GUI for the DELPHI - Fix A/B axes direction in lens alignment tab of the SECOMv1. This might require to inverse (back) the A/B axes in the microscope file. - Optical/SEM views have been switched to put the optical view, which is used first, on the top/left. -- Éric Piel (Delmic) Wed, 14 Jan 2015 23:48:35 +0100 odemis (1.8-1ubuntu1) precise; urgency=low * New version: 1.8 * Main new features: - Support for the DELPHI - Direct selection of the hardware settings for excitation and emission wavelengths in filtered colour streams (SECOM/DELPHI) - History of the stage positions and possibility to move based on the overview image (SECOM/DELPHI) - Use "Screen" blending to merge multiple filtered colour streams (SECOM/DELPHI) - Background subtraction option for spectra (SPARC) - SEM view HFW is linked to the actual SEM HFW (DELPHI) - Support for connecting to PI controllers over IP * Main bugs fixed and improvements: - Autofocus can be run from the toolbar, and can be interrupted (SECOM/DELPHI) - Fix latency issue with Andor sCMOS cameras (for Neo and Zyla cameras) - Allow up to 500s acquisition time for the CCDs (SPARC) - Anchor region is scanned at least every 10s, to improve drift correction (SPARC) - Add vertical center line in goal image for easier alignment (SPARC) - Shortcut to "Stop all axes" is now Pause, instead of ESC (which is used in other places) - Add referencing procedure to the TMCM driver and support it in odemis-cli - Reduce latency in focus move (mainly visible on closed-loop actuators such as DELPHI) - Rename CombinedActuator to MultiplexActuator - Now works with wx3.0, latest stable version instead of wx2.9 -- Éric Piel (Delmic) Wed, 08 Oct 2014 10:54:09 +0200 odemis (1.7-1ubuntu1) precise; urgency=low * New version: 1.7 * Main new features: * Rotate optical images based on the fine alignment result (SECOM) * Automatic spot alignment procedure (SECOM) * Autofocus function (SECOM) * Support changing filters on the SPARC * Display average spectrum count over the last 30s (SPARC) * Support for Thorlabs lens mount (SPARC) * Add more menu entries and shortcut to manipulate the streams * Turn off camera fan during high quality acquisition (SECOM) * Beta support for managing SEM chamber pressure * Beta support for Phenom SEMs * Alpha suport for Tescan SEMs * Support for Trinamic stages * Main bug fixed and improvements: * Simplify Optical/SEM on/off buttons (SECOM) * Allow dwell time > 30s on SEM external scanner (semcomedi) * Fine alignment handles very small and very large SEM magnification (SECOM) * Allow to reset the fine alignment data * Handle very large AR polar projections (SPARC) * Rotation metadata saved in TIFF and HDF5 format (SECOM) * Ensure the anchor region is never too high resolution (SPARC) * If the acquisition fails, all the images already acquired are saved -- Éric Piel (Delmic) Tue, 15 Jul 2014 17:37:23 +0200 odemis (1.6-1ubuntu1) precise; urgency=low * New version: 1.6 * Main new features: * Fine alignment (SECOM) * Drift correction (SPARC) * Support for the Andor SR303i spectrometer (requires latest Andor SDK2) * Angular resolved background image subtraction (SPARC) * Spectrum efficiency correction (SPARC) * Graph of intensity over time in spectrum settings (SPARC) * Simulated SEM with drift * Option to save current gallery image under a new name/format * Odemis-viewer: new launcher to view previous acquisitions without a microscope connected * Main bug fixed and improvements: * Reduced latency in displaying (large) live images * Do not start optical microscope with maximum light power (SECOM) * During acqusition, schedule fluo streams with long emission wl first (SECOM) * Many small GUI improvements * Udev rules are now placed in /lib instead of /etc -- Éric Piel (Delmic) Mon, 07 Apr 2014 15:37:23 +0200 odemis (1.5-1ubuntu1) precise; urgency=low * New version: 1.5 * Main new features: - Support for Thorlab filter wheel FW102C - Automatically select the right filter if a filter wheel is used (SECOM) - Support for the Andor Zyla - Support for the Andor iDus - Spectrum display also displays the Y values (SPARC) - ebeam can be parked outside of the SEM field of view * Main bug fixed: - Spot mode was sometimes having a second weaker spot - Lumencor Light Engine driver doesn't mistake device - On 64 bits, some metadata where not saved in HDF5 - Saving tiff file with a non-ascii character in a name failed - Polar projection of large image consumed too much memory (SPARC) - Large exposure times are displayed correctly in the settings (SECOM) - Display of just one AR image is displayed correctly (SPARC) - Cannot quit the GUI by mistake during a SPARC acquisition (SPARC) - Goal image for mirror alignment depends on the CCD size (SPARC) -- Éric Piel (Delmic) Fri, 14 Feb 2014 14:02:25 +0100 odemis (1.4-1ubuntu8) precise; urgency=low * Clean up build/ directory which is messing if left from previous builds * Change directory location for doc from develop to more convential develop-html -- Éric Piel (Delmic) Thu, 02 Jan 2014 11:59:52 +0100 odemis (1.4-1ubuntu7) precise; urgency=low * Actually call inkscape from the debian/rules so that the PDF figures are generated -- Éric Piel (Delmic) Thu, 02 Jan 2014 10:45:48 +0100 odemis (1.4-1ubuntu6) precise; urgency=low * More build trial for latex, with inkscape -- Éric Piel (Delmic) Tue, 31 Dec 2013 18:07:43 +0100 odemis (1.4-1ubuntu5) precise; urgency=low * Another rebuild for latex... -- Éric Piel (Delmic) Mon, 30 Dec 2013 08:15:14 +0100 odemis (1.4-1ubuntu4) precise; urgency=low * Rebuild, hoping to really fix the latex build dep -- Éric Piel (Delmic) Sun, 29 Dec 2013 23:42:54 +0100 odemis (1.4-1ubuntu3) precise; urgency=low * Rebuild with build dependencies for pdflatex (to build the PDF documentation) -- Éric Piel (Delmic) Wed, 25 Dec 2013 17:42:46 +0100 odemis (1.4-1ubuntu2) precise; urgency=low * Rebuild for documentation build fix (couldn't find the version number) -- Éric Piel (Delmic) Tue, 24 Dec 2013 18:25:14 +0100 odemis (1.4-1ubuntu1) precise; urgency=low * New version: 1.4 * Main new features: - Support for angular-resolved acquisition on SPARC - Display of angular-resolved acquisition in polar view - Spectrum display of a point (on the SPARC) - Support for Andor Neo on SPARC - Support for EMCCD Andor cameras - Ability to have a SPARC with only a spectrometer or only a AR camera - Ability to change light power (SECOM) - Improved fine stage movement with PI actuators (SECOM) - Basic support for Omicron xX laser sources - Developer documentation - Auto-completion of odemis-cli arguments * Main bug fixed: - Support SEM dwell times > 0.8s (now arbitrarily limited to < 100s) - Automatic button in dichotomy-based lens alignment moves to the right direction - Improved High Quality preset in SECOM acquisition - Image with all values at the maximum displays white (instead of black) - Keep the region of acquisition proportional when changing SEM magnification (SPARC) - Limit log of backend to 500 Mb - Stable SEM/CCD synchronised acquisition with improved time estimation -- Éric Piel (Delmic) Tue, 24 Dec 2013 14:35:44 +0100 odemis (1.3-1ubuntu1) precise; urgency=low * New version: 1.3 * Main new features: - Lens alignment tab for manual calibration of the SECOM - Can open back previsou acquisitions in OME TIFF format too - Enhanced management of the contrast and brightness with small histrogram - Fit to RGB display option for the acquired spectra in SPARC - Graphical representation repetition in the SPARC acquisition - Large indicator icon when streams are paused - Display manual on the press of F1 - Allow to rotate/flip CCD input in software - Allow calibration of PI actuator controllers * Main bug fixed: - fix SEM acquisition with minimum dwell time - ensure the light source is off during SEM acquisition - many improvement in the way HDF5 files are re-opened - improved High Quality preset in SECOM acquisition -- Éric Piel (Delmic) Fri, 27 Sep 2013 22:21:17 +0200 odemis (1.2-1ubuntu1) precise; urgency=low * New version: 1.2 * Main new features: - can open back acquisition previous files (only for HDF5 format) - SPARC manual mirror alignment interface - improved GUI control for the wavelength of spectra - can be used without any microscope connected (for example for opening back a file) - can be installed using the normal python way (setup.py) - include some examples of Python scripts using odemis * Main bug fixed - fix scanning area of SEM twice too large - fix SEM-CL acquisition sometime not receiving all the pixels -- Éric Piel (Delmic) Sat, 29 Jun 2013 20:16:32 +0200 odemis (1.2~alpha3-1ubuntu1) precise; urgency=low * Package documentation too * Improvements to the GUI: - Mirror Alignment tab should work fully - Allow to open back an previous acquisition -- Éric Piel (Delmic) Mon, 24 Jun 2013 15:14:19 +0200 odemis (1.2~alpha2-1ubuntu1) precise; urgency=low * Package necessary data * Some improvements on the calibration tab + anaylisis tab for the SPARC -- Éric Piel (Delmic) Mon, 17 Jun 2013 17:00:40 +0200 odemis (1.2~alpha1-1ubuntu1) precise; urgency=low * Fix build dependencies -- Éric Piel (Delmic) Tue, 11 Jun 2013 10:07:33 +0200 odemis (1.2~alpha1-1) precise; urgency=low * Initial release (alpha release pre 1.2) -- Éric Piel (Delmic) Mon, 10 Jun 2013 16:19:03 +0600