Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Reworking LMSMetadata package and adding a new lif reader #4000

Open
wants to merge 94 commits into
base: develop
Choose a base branch
from
Open

Reworking LMSMetadata package and adding a new lif reader #4000

wants to merge 94 commits into from

Commits on Jan 2, 2023

  1. LOFReader: ome#3818 LOF file error; [Fatal Error] :1:1: Content is no… 

    …t allowed in prolog.

adapted error messaging
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 2, 2023
    Configuration menu
    Copy the full SHA
    a7874d0 View commit details
    Browse the repository at this point in the history

Commits on Jan 4, 2023

  1. LIFReader: ome#3655 Incorrect channel colours, adding LIFReader2 whic… 

    …h uses LMS metadata classes (pending discussion).

temporary changes to LIFReader.isThisType() and readers.txt to use LIFReader2 instead of LIFReader for testing
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 4, 2023
    Configuration menu
    Copy the full SHA
    d27015b View commit details
    Browse the repository at this point in the history

Commits on Jan 17, 2023

  1. LMS metadata package: started rework of metadata translation

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 17, 2023
    Configuration menu
    Copy the full SHA
    16486c8 View commit details
    Browse the repository at this point in the history

  2. Merge remote-tracking branch 'upstream/develop' into xlefreader

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 17, 2023
    Configuration menu
    Copy the full SHA
    39af6a1 View commit details
    Browse the repository at this point in the history

Commits on Jan 20, 2023

  1. LMS metadata package: reworking stand details, objective, lasers, det… 

    …ectors and filters translation
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 20, 2023
    Configuration menu
    Copy the full SHA
    20575a4 View commit details
    Browse the repository at this point in the history

Commits on Jan 23, 2023

  1. LMS metadata package: mapping of detector information from LDM block … 

    …sequential list to channel detector settings
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 23, 2023
    Configuration menu
    Copy the full SHA
    84784a9 View commit details
    Browse the repository at this point in the history

Commits on Jan 24, 2023

  1. LMS metadata package: mapping multiband / filter info from sequential… 

    … blocks to detector settings and channels
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 24, 2023
    Configuration menu
    Copy the full SHA
    8e2eae0 View commit details
    Browse the repository at this point in the history

  2. LMS metadata package: formatting, author/copyright

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 24, 2023
    Configuration menu
    Copy the full SHA
    7fa742c View commit details
    Browse the repository at this point in the history

Commits on Jan 25, 2023

  1. rename LIFReader2, LMS metadata package: setting up new structure / a… 

    …rchitecture (in progress)
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 25, 2023
    Configuration menu
    Copy the full SHA
    755eb2a View commit details
    Browse the repository at this point in the history

Commits on Jan 26, 2023

  1. LMS metadata package: reworking channel and dimension metadata handling

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 26, 2023
    Configuration menu
    Copy the full SHA
    b2589fd View commit details
    Browse the repository at this point in the history

  2. LMSMetadataPackage: setting up usage of new classes

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 26, 2023
    Configuration menu
    Copy the full SHA
    5ee1b3a View commit details
    Browse the repository at this point in the history

Commits on Jan 27, 2023

  1. LMS metadata package: moving channel, dimension and position related … 

    …info translation
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 27, 2023
    Configuration menu
    Copy the full SHA
    ab87d87 View commit details
    Browse the repository at this point in the history

Commits on Feb 13, 2023

  1. Merge branch 'ome:develop' into xlefreader

    @XLEFReaderForBioformats
    XLEFReaderForBioformats authored Feb 13, 2023
    Configuration menu
    Copy the full SHA
    0b7d202 View commit details
    Browse the repository at this point in the history

  2. LMSMetadata package: i.a. fixing filter and laser settings and physic… 

    …al Z size translation
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 13, 2023
    Configuration menu
    Copy the full SHA
    aa5419e View commit details
    Browse the repository at this point in the history

Commits on Feb 14, 2023

  1. Merge branch 'ome:develop' into xlefreader

    @XLEFReaderForBioformats
    XLEFReaderForBioformats authored Feb 14, 2023
    Configuration menu
    Copy the full SHA
    390c359 View commit details
    Browse the repository at this point in the history

  2. LMSMetadata package: detector read out rate, laser channel mapping di… 

    …stinguishes between SPX and STELLARIS, fixing channelPrios for LIF/LOF
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 14, 2023
    Configuration menu
    Copy the full SHA
    9bfcea7 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'ome:develop' into xlefreader

    @XLEFReaderForBioformats
    XLEFReaderForBioformats authored Feb 14, 2023
    Configuration menu
    Copy the full SHA
    d2b1c74 View commit details
    Browse the repository at this point in the history

Commits on Feb 17, 2023

  1. LMS metadata package: removing LMSMetadataExtractor, MetadataStoreIni… 

    …tializer, MetadataTempBuffer
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 17, 2023
    Configuration menu
    Copy the full SHA
    94f5da0 View commit details
    Browse the repository at this point in the history

Commits on Feb 22, 2023

  1. Merge branch 'ome:develop' into xlefreader

    @XLEFReaderForBioformats
    XLEFReaderForBioformats authored Feb 22, 2023
    Configuration menu
    Copy the full SHA
    27182f8 View commit details
    Browse the repository at this point in the history

  2. LMSMetadata package: ignoring laser settings with intensitydev=0

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 22, 2023
    Configuration menu
    Copy the full SHA
    0861cd5 View commit details
    Browse the repository at this point in the history

  3. LMSMetadata package: bugfix swapXY

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 22, 2023
    Configuration menu
    Copy the full SHA
    2cd0510 View commit details
    Browse the repository at this point in the history

Commits on Feb 28, 2023

  1. LMSMetadata package: fixing physical z sizes / positions

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    e692e55 View commit details
    Browse the repository at this point in the history

  2. LMSMetadata package: renaming Translator

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    3385a23 View commit details
    Browse the repository at this point in the history

Commits on Mar 1, 2023

  1. LMSMetadata package: bugfix Z positions

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 1, 2023
    Configuration menu
    Copy the full SHA
    d475982 View commit details
    Browse the repository at this point in the history

Commits on Mar 3, 2023

  1. LMSMetadata package: bugfixes for LIF XML image nodes finding, empty … 

    …instruments for images without hardware settings, empty timestamps, correct interleaving depending on image format
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 3, 2023
    Configuration menu
    Copy the full SHA
    9a5866a View commit details
    Browse the repository at this point in the history

Commits on Mar 6, 2023

  1. LMSMetadata package: refactoring channel priorities / lut color index

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 6, 2023
    Configuration menu
    Copy the full SHA
    f7eadbb View commit details
    Browse the repository at this point in the history

Commits on Mar 20, 2023

  1. LMSMetadata package: bugfix z position extraction and z position per … 

    …plane calculation, adding z drive modes
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 20, 2023
    Configuration menu
    Copy the full SHA
    dbed0d5 View commit details
    Browse the repository at this point in the history

Commits on Apr 27, 2023

  1. LMSMetadataPackage: also allow basic metadata translation of SP5 images

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Apr 27, 2023
    Configuration menu
    Copy the full SHA
    710e8da View commit details
    Browse the repository at this point in the history

  2. Merge branch 'ome:develop' into xlefreader

    @XLEFReaderForBioformats
    XLEFReaderForBioformats authored Apr 27, 2023
    Configuration menu
    Copy the full SHA
    e65427c View commit details
    Browse the repository at this point in the history

Commits on May 2, 2023

  1. LMSMetadataPackage: translate filters and exposure times for sequenti… 

    …al and non-sequential widefield images
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed May 2, 2023
    Configuration menu
    Copy the full SHA
    668b77e View commit details
    Browse the repository at this point in the history

  2. Merge branch 'ome:develop' into xlefreader

    @XLEFReaderForBioformats
    XLEFReaderForBioformats authored May 2, 2023
    Configuration menu
    Copy the full SHA
    7de6ebe View commit details
    Browse the repository at this point in the history

Commits on May 3, 2023

  1. LMSMetadataPackage: adding (doc) comments

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed May 3, 2023
    Configuration menu
    Copy the full SHA
    210bf56 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'ome:develop' into xlefreader

    @XLEFReaderForBioformats
    XLEFReaderForBioformats authored May 3, 2023
    Configuration menu
    Copy the full SHA
    7cb2e2d View commit details
    Browse the repository at this point in the history

Commits on May 4, 2023

  1. Merge branch 'ome:develop' into xlefreader

    @XLEFReaderForBioformats
    XLEFReaderForBioformats authored May 4, 2023
    Configuration menu
    Copy the full SHA
    6ea8198 View commit details
    Browse the repository at this point in the history

  2. Reverting temporary changes to LIFReader.isThisType(...) for testing

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed May 4, 2023
    Configuration menu
    Copy the full SHA
    8a23660 View commit details
    Browse the repository at this point in the history

  3. reverting mapping from .lif files to LMSLIFReader instead of LIFReader

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed May 4, 2023
    Configuration menu
    Copy the full SHA
    8a5f235 View commit details
    Browse the repository at this point in the history

Commits on Jan 22, 2024

  1. Merge branch 'ome:develop' into xlefreader

    @XLEFReaderForBioformats
    XLEFReaderForBioformats authored Jan 22, 2024
    Configuration menu
    Copy the full SHA
    97c25c9 View commit details
    Browse the repository at this point in the history

Commits on Jan 24, 2024

  1. temporarily deactivating LIFReader for LMSLifReader testing

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    1e773e2 View commit details
    Browse the repository at this point in the history

  2. fixing bugs: handling images without hardware settings attachment, wr… 

    …ong pixel rendering, rgb reordering.

also some refactoring
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    cc2ce7f View commit details
    Browse the repository at this point in the history

  3. refactoring: 1 folder for core / OME metadata writers

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    f78233c View commit details
    Browse the repository at this point in the history

  4. refactoring: missing package reference adjustments

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    8b7a2ad View commit details
    Browse the repository at this point in the history

  5. fix xml parsing sequential camera settings

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    951588b View commit details
    Browse the repository at this point in the history

Commits on Jan 26, 2024

  1. LMSLIFReader, LOFReader: accessing inverse rgb for correct image (for… 

    … normal images and tilescans)
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 26, 2024
    Configuration menu
    Copy the full SHA
    4056876 View commit details
    Browse the repository at this point in the history

Commits on Jan 31, 2024

  1. supporting MICA confocal, widefield and widefocal images

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 31, 2024
    Configuration menu
    Copy the full SHA
    a57dfb9 View commit details
    Browse the repository at this point in the history

  2. further adjustments for support of MICA CS/WF/WFO images

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Jan 31, 2024
    Configuration menu
    Copy the full SHA
    352f549 View commit details
    Browse the repository at this point in the history

Commits on Feb 5, 2024

  1. fixing bug in timestamp extraction

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 5, 2024
    Configuration menu
    Copy the full SHA
    9e1d0d1 View commit details
    Browse the repository at this point in the history

Commits on Feb 6, 2024

  1. supporting different hardware setting setups, adding dye information … 

    …to channels in MICA images
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 6, 2024
    Configuration menu
    Copy the full SHA
    268bf4f View commit details
    Browse the repository at this point in the history

Commits on Feb 9, 2024

  1. reworking handling of hardware setting layouts varying with different… 

    … imaging systems
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 9, 2024
    Configuration menu
    Copy the full SHA
    570c716 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'ome:develop' into xlefreader

    @XLEFReaderForBioformats
    XLEFReaderForBioformats authored Feb 9, 2024
    Configuration menu
    Copy the full SHA
    035946a View commit details
    Browse the repository at this point in the history

  3. fixing bug in detector settings translation

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 9, 2024
    Configuration menu
    Copy the full SHA
    47afe80 View commit details
    Browse the repository at this point in the history

Commits on Feb 12, 2024

  1. adjusting translation of detectors and detector settings, also writin… 

    …g dye names to channels
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 12, 2024
    Configuration menu
    Copy the full SHA
    1ae0e6e View commit details
    Browse the repository at this point in the history

Commits on Feb 13, 2024

  1. reworking filter (set) creation, using channel > lightpath > emission… 

    …filterref instead of channel > filtersetref
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 13, 2024
    Configuration menu
    Copy the full SHA
    901d1b3 View commit details
    Browse the repository at this point in the history

Commits on Feb 21, 2024

  1. major rework of instrument / channel settings translation 

    bundled extraction of sequential acquisition settings, regarding different laser types, slightly simplified architecture
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    8b3c4be View commit details
    Browse the repository at this point in the history

  2. remove unused imports

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    fffb6b4 View commit details
    Browse the repository at this point in the history

  3. fix bug in widefield images (main camera setting not set)

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    59a7d02 View commit details
    Browse the repository at this point in the history

Commits on Feb 22, 2024

  1. regarding lasers which are not coupled to AOTFs, shutters, light sour… 

    …ce types and laser power states
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 22, 2024
    Configuration menu
    Copy the full SHA
    0927e28 View commit details
    Browse the repository at this point in the history

Commits on Feb 23, 2024

  1. major refactoring of SingleImageTranslator to prepare separate calls … 

    …of extract() and write() for tile scans
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 23, 2024
    Configuration menu
    Copy the full SHA
    c054667 View commit details
    Browse the repository at this point in the history

Commits on Feb 26, 2024

  1. core and store metadata are now correctly written for image tiles

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 26, 2024
    Configuration menu
    Copy the full SHA
    9ff6cdc View commit details
    Browse the repository at this point in the history

  2. fixing timestamp / plane deltaT bug: is now correctly translated

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 26, 2024
    Configuration menu
    Copy the full SHA
    62d6962 View commit details
    Browse the repository at this point in the history

Commits on Feb 27, 2024

  1. adding collection path to image name (LIF and XLEF)

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 27, 2024
    Configuration menu
    Copy the full SHA
    c19fb6d View commit details
    Browse the repository at this point in the history

  2. fix build

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 27, 2024
    Configuration menu
    Copy the full SHA
    84ee004 View commit details
    Browse the repository at this point in the history

  3. bugfix: widefield atl setting empty

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 27, 2024
    Configuration menu
    Copy the full SHA
    515b212 View commit details
    Browse the repository at this point in the history

  4. adding translation of objective correction

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 27, 2024
    Configuration menu
    Copy the full SHA
    1a93dbc View commit details
    Browse the repository at this point in the history

  5. avoiding crash for SP5 images without LDM block / atl settings

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 27, 2024
    Configuration menu
    Copy the full SHA
    3abcb0d View commit details
    Browse the repository at this point in the history

Commits on Feb 28, 2024

  1. fixing laser isActive logic

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 28, 2024
    Configuration menu
    Copy the full SHA
    1043971 View commit details
    Browse the repository at this point in the history

Commits on Feb 29, 2024

  1. fixing bug: crash on unformatted objective name

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 29, 2024
    Configuration menu
    Copy the full SHA
    5494b4c View commit details
    Browse the repository at this point in the history

  2. getting data source type for SP5 images without atl settings

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 29, 2024
    Configuration menu
    Copy the full SHA
    2955318 View commit details
    Browse the repository at this point in the history

  3. adding lasers for SP5 images without ATL settings

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 29, 2024
    Configuration menu
    Copy the full SHA
    e50969f View commit details
    Browse the repository at this point in the history

  4. getting instrument detectors for SP5 images without atl settings

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Feb 29, 2024
    Configuration menu
    Copy the full SHA
    f1be021 View commit details
    Browse the repository at this point in the history

Commits on Mar 4, 2024

  1. adding immersion and correction lookup functions from objective name … 

    …string (which is not as formatted as assumed)
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 4, 2024
    Configuration menu
    Copy the full SHA
    73be214 View commit details
    Browse the repository at this point in the history

  2. confocal settings extraction: major rework to support reading from ei… 

    …ther ATL settings or from scanner / filter setting records

if scanner / filter settings exist, they are parsed, information is stored in ConfocalSettingRecords for easy access. separating ATL settings and setting records logic
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 4, 2024
    Configuration menu
    Copy the full SHA
    a5c1d1e View commit details
    Browse the repository at this point in the history

Commits on Mar 5, 2024

  1. refactoring folders / names

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    f266ab8 View commit details
    Browse the repository at this point in the history

  2. adding channel settings with lasers for SP5 images, support of MP las… 

    …ers / NDD detectors
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    9f96fea View commit details
    Browse the repository at this point in the history

  3. SP5 images without atl settings: mapping detectors to detector settings

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    bb2494e View commit details
    Browse the repository at this point in the history

  4. adapting shutter check

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    d02d6db View commit details
    Browse the repository at this point in the history

Commits on Mar 11, 2024

  1. parsing shutter info from confocal setting records

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 11, 2024
    Configuration menu
    Copy the full SHA
    35a804a View commit details
    Browse the repository at this point in the history

  2. getting correct detector / filter names for SP5 images with and witho… 

    …ut ATL settings
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 11, 2024
    Configuration menu
    Copy the full SHA
    c0d2c38 View commit details
    Browse the repository at this point in the history

  3. adding objective from confocal setting records

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 11, 2024
    Configuration menu
    Copy the full SHA
    04b2d0a View commit details
    Browse the repository at this point in the history

Commits on Mar 12, 2024

  1. creating LIFDelegateReader so usage of LIFReader and LMSLIFReader can… 

    … be toggled
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    06542f2 View commit details
    Browse the repository at this point in the history

  2. correct plane deltaTs and xy positions for RGB images

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    fb01a07 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'ome:develop' into xlefreader

    @XLEFReaderForBioformats
    XLEFReaderForBioformats authored Mar 12, 2024
    Configuration menu
    Copy the full SHA
    57b4544 View commit details
    Browse the repository at this point in the history

Commits on Mar 13, 2024

  1. class javadoc + copyright comments

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    8d12cda View commit details
    Browse the repository at this point in the history

  2. rename folder, name might be confusing

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    ad8d8d6 View commit details
    Browse the repository at this point in the history

  3. correct references

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    0f7ede5 View commit details
    Browse the repository at this point in the history

Commits on Mar 14, 2024

  1. increasing robustness against missing / unexpected data, preventing e… 

    …xceptions
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 14, 2024
    Configuration menu
    Copy the full SHA
    cca1703 View commit details
    Browse the repository at this point in the history

Commits on Mar 25, 2024

  1. using posZ attribute in tile scan info, if available

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 25, 2024
    Configuration menu
    Copy the full SHA
    bac07f8 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'ome:develop' into xlefreader

    @XLEFReaderForBioformats
    XLEFReaderForBioformats authored Mar 25, 2024
    Configuration menu
    Copy the full SHA
    9e40086 View commit details
    Browse the repository at this point in the history

Commits on Mar 26, 2024

  1. bugfix: in LIF files containing "invalid" memory blocks (e.g. "frame … 

    …properties"), wrong image offsets are used

mapping of memory blocks to images found in XML via memory block ids, removing offsets of "invalid" memory blocks.
frame properties and other children of image nodes are not considered valid images
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Mar 26, 2024
    Configuration menu
    Copy the full SHA
    47cbf13 View commit details
    Browse the repository at this point in the history

Commits on Apr 3, 2024

  1. fixing mapping of WLLs to laser line settings

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Apr 3, 2024
    Configuration menu
    Copy the full SHA
    dee599e View commit details
    Browse the repository at this point in the history

Commits on Apr 10, 2024

  1. translating Z range / position for SP5 images without ATL settings

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Apr 10, 2024
    Configuration menu
    Copy the full SHA
    32147d2 View commit details
    Browse the repository at this point in the history

  2. bug fix zEnd calculation

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Apr 10, 2024
    Configuration menu
    Copy the full SHA
    dfaf67f View commit details
    Browse the repository at this point in the history

Commits on Oct 28, 2024

  1. Merge branch 'ome:develop' into xlefreader

    @XLEFReaderForBioformats
    XLEFReaderForBioformats authored Oct 28, 2024
    Configuration menu
    Copy the full SHA
    53a7a99 View commit details
    Browse the repository at this point in the history

  2. fixing IndexOutOfBoundsException in LMSLIFReader.initFile()

    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Oct 28, 2024
    Configuration menu
    Copy the full SHA
    d3e5abf View commit details
    Browse the repository at this point in the history

  3. fixing NullPointerException in ConfocalSettingsFromSettingRecordsExtr… 

    …actor.createChannelSettings(..)
    @XLEFReaderForBioformats
    XLEFReaderForBioformats committed Oct 28, 2024
    Configuration menu
    Copy the full SHA
    105fd8a View commit details
    Browse the repository at this point in the history