MathOnco/valis issues and pull requests

#75 - Annotations transferred with VALIS cannot be modified (despite being unlocked)

Issue - State: closed - Opened by marco1108 over 1 year ago

#74 - UnboundLocalError: local variable 'reader' referenced before assignment

Issue - State: closed - Opened by WXY-Belief over 1 year ago - 2 comments

#73 - after registration, parameters for rigid registration

Issue - State: closed - Opened by WXY-Belief over 1 year ago - 3 comments

#72 - Increased epsilon value in norm_img_stats

Pull Request - State: closed - Opened by NichD over 1 year ago

#71 - Non-monotonically increasing image values cause error in normalization

Issue - State: closed - Opened by NichD over 1 year ago - 2 comments

#70 - Rigid registration attempts impossible warps

Issue - State: open - Opened by dnschouten over 1 year ago - 1 comment

#69 - Update ACROBAT README.rst

Pull Request - State: closed - Opened by cdgatenbee over 1 year ago

#68 - rigid registration not working

Issue - State: closed - Opened by matthiaskoenig over 1 year ago - 2 comments

#67 - extract_area: bad extract area Error

Issue - State: open - Opened by matthiaskoenig over 1 year ago - 7 comments

#66 - Fix docker link

Pull Request - State: closed - Opened by matthiaskoenig over 1 year ago

#65 - Error in local Docker build

Issue - State: closed - Opened by dnschouten over 1 year ago - 1 comment

#64 - xmlschema.exceptions error on Windows WSL only

Issue - State: closed - Opened by Raoufsk over 1 year ago - 3 comments

#63 - Applying tranformations from the registrar to other slides.

Issue - State: closed - Opened by Gibbsdavidl over 1 year ago - 3 comments

#60 - Problem: Reading the high-resolution layers of the pyramid image for registration at a lower resolution level.

Issue - State: open - Opened by juanenofbit over 1 year ago - 16 comments

#59 - Registering Slide to Standard Space

Issue - State: open - Opened by abadgerw over 1 year ago - 27 comments

#57 - scaling transformation for image with different shape

Issue - State: closed - Opened by batukav over 1 year ago - 8 comments

#56 - Ome.tif write time

Issue - State: open - Opened by ajr82 over 1 year ago - 13 comments

#55 - SLF4J error and query about max_image_dim_pix and max_processed_image_dim_pix

Issue - State: open - Opened by teacakedeadlift over 1 year ago - 14 comments

#54 - readthedocs: image_type class init: img_type

Issue - State: closed - Opened by Gibbsdavidl over 1 year ago - 1 comment

#53 - subprocess.CalledProcessError

Issue - State: open - Opened by halynyu over 1 year ago - 5 comments

#52 - warp and save slides failing

Issue - State: closed - Opened by Gibbsdavidl over 1 year ago - 3 comments

#51 - Learn transformation on one image pair and apply to the rest.

Issue - State: closed - Opened by myylee almost 2 years ago - 5 comments

#50 - micro registration failing

Issue - State: closed - Opened by GlastonburyC almost 2 years ago - 11 comments

#49 - Apply registration to new image

Issue - State: closed - Opened by Celestenono almost 2 years ago - 3 comments

#48 - aligning two H&E files

Issue - State: closed - Opened by GlastonburyC almost 2 years ago - 2 comments

#47 - Error when running micro registration

Issue - State: closed - Opened by daviddaiweizhang almost 2 years ago - 5 comments

#46 - Minor improvements

Pull Request - State: closed - Opened by ajinkya-kulkarni almost 2 years ago

#45 - HE and H-DAB sections - alignment and ? merge

Issue - State: open - Opened by teacakedeadlift almost 2 years ago - 3 comments

#44 - Mask generation failing on select sub-tiles

Issue - State: closed - Opened by NichD almost 2 years ago - 12 comments

#43 - ``None`` option for norm_method argument

Pull Request - State: closed - Opened by aelskens almost 2 years ago

#42 - H&E deconvolution

Pull Request - State: closed - Opened by aelskens almost 2 years ago

#41 - H&E deconvolution pre-processing

Issue - State: closed - Opened by aelskens almost 2 years ago - 6 comments

#40 - In register_micro() (registration.py), shouldn't new_bk_dxdy be a vips image?

Issue - State: closed - Opened by zindy almost 2 years ago - 3 comments

#39 - keyword "max_non_rigid_registartion_dim_px" misspelled

Issue - State: closed - Opened by zindy almost 2 years ago - 1 comment

#36 - `match_desc_and_kp` possibly missing `max_ratio` argument

Issue - State: closed - Opened by idc9 about 2 years ago - 1 comment

#35 - error calling register on 2 svs files

Issue - State: open - Opened by idc9 about 2 years ago - 1 comment
Labels: stale

#34 - Issue in installing Valis-WSI

Issue - State: closed - Opened by marco1108 about 2 years ago - 11 comments

#33 - Unable to run the example

Issue - State: closed - Opened by JACKCHAN000 about 2 years ago - 7 comments

#30 - Intermittent artifacts introduced in micro-registration step

Issue - State: closed - Opened by NichD about 2 years ago - 6 comments

#29 - AttributeError: vips_image_hasalpha

Issue - State: closed - Opened by q1nwu about 2 years ago - 1 comment

#28 - Unable to initialize valis-wsi due to Maven/toolchain config issue

Issue - State: open - Opened by NichD over 2 years ago - 9 comments

#27 - Registration within selected ROIs

Issue - State: closed - Opened by anranli0 over 2 years ago - 3 comments

#26 - YCbCr colorspace from pyvips jp2k/jpeg compression causes brightfield/RGB ome.tiff image results to look pink when opening in QuPath

Issue - State: closed - Opened by snibbor over 2 years ago - 3 comments

#25 - Pixel errors in the registered images in regions w/ high intensity values

Issue - State: open - Opened by cwenge over 2 years ago - 9 comments
Labels: stale

#24 - not enough points to transform

Issue - State: closed - Opened by NicolasNerr over 2 years ago - 1 comment

#23 - keep original colors for channels if they are within metadata. input channel color map as option

Issue - State: closed - Opened by snibbor over 2 years ago - 3 comments

#22 - how to handle aligning images that are mirrored/flipped automatically

Issue - State: closed - Opened by snibbor over 2 years ago - 6 comments

#19 - File size increasing 10 times after registrations

Issue - State: closed - Opened by tkobayashi6 over 2 years ago - 1 comment

#18 - dependencies issue

Issue - State: closed - Opened by NicolasNerr over 2 years ago - 5 comments

#17 - Reproducing Acrobat2022 Results

Issue - State: closed - Opened by batukav over 2 years ago - 4 comments

#16 - pyvips.error.Error: affine does not support optional argument premultiplied

Issue - State: closed - Opened by tkobayashi6 over 2 years ago - 8 comments

#14 - Precomputed rigid transformation passed as a dictionary in the "do_rigid" argument

Issue - State: closed - Opened by juanenofbit over 2 years ago - 11 comments

#13 - QuPath Annotation Transfer

Issue - State: closed - Opened by abadgerw over 2 years ago - 44 comments
Labels: enhancement

#12 - Non Rigid Registration Error

Issue - State: closed - Opened by Tejussurendran over 2 years ago - 11 comments

#11 - patched some of the code to work with saving uint16 IF .ome.tifs

Pull Request - State: closed - Opened by snibbor over 2 years ago - 1 comment

#10 - No conversion from UniTuple(array(int64, 1d, C) x 2) to UniTuple(array(int32, 1d, C) x 2) for '$376return_value.9', defined at None

Issue - State: closed - Opened by snibbor over 2 years ago - 4 comments

#9 - fix conversion error when importing viz

Pull Request - State: closed - Opened by zindy over 2 years ago - 1 comment

#8 - numpy.AxisError: axis 2 is out of bounds for array of dimension 2

Issue - State: closed - Opened by MNM-TB over 2 years ago - 6 comments

#7 - Error running basic example

Issue - State: closed - Opened by cwenge over 2 years ago - 6 comments

#6 - Initialize is_flattended_pyramid variable to False

Pull Request - State: closed - Opened by Jose-Verdu-Diaz almost 3 years ago - 1 comment

#5 - Local variable 'is_flattended_pyramid' referenced before assignment

Issue - State: closed - Opened by Jose-Verdu-Diaz almost 3 years ago - 2 comments
Labels: bug

#4 - create ci yaml

Pull Request - State: closed - Opened by cdgatenbee about 3 years ago

#3 - Add .circleci/config.yml

Pull Request - State: closed - Opened by cdgatenbee about 3 years ago

#1 - Update index.rst

Pull Request - State: closed - Opened by cdgatenbee about 3 years ago

GitHub / MathOnco/valis issues and pull requests