MathOnco/valis issues and pull requests

#163 - facing issue in non_rigid_registrars.NonRigidRegistrar

Issue - State: open - Opened by shubhankar-git 2 months ago

#162 - facing error using NonRigidRegistrarGroupwise

Issue - State: open - Opened by shubhankar-git 2 months ago

#161 - error using SimpleElastixWarper

Issue - State: open - Opened by shubhankar-git 2 months ago

#160 - Issues with points - not transformed correctly?

Issue - State: open - Opened by lukasz-migas 2 months ago

#159 - Zen 3.8+ Incompatibility

Issue - State: open - Opened by Justin-Krieg 2 months ago - 1 comment

#158 - Docker usage generates nonsensical image

Issue - State: closed - Opened by Justin-Krieg 2 months ago - 1 comment

#157 - register problem

Issue - State: open - Opened by lingxitong 2 months ago

#156 - Specify Channel Order When Merging

Issue - State: closed - Opened by ewestlundicr 3 months ago - 2 comments
Labels: question

#155 - Save only one Tiff

Issue - State: closed - Opened by lingxitong 3 months ago - 4 comments

#154 - Extracting transformation matrix and applying on other images.

Issue - State: open - Opened by simomounir 3 months ago - 1 comment

#153 - Processing Images with Low Brightness and Contrast

Issue - State: open - Opened by ignaciojci 3 months ago - 1 comment

#152 - Unable to reproduce results in register_ihc.py example

Issue - State: open - Opened by changwxx 3 months ago - 5 comments

#151 - Saving as .ome.tiff

Issue - State: open - Opened by snackthingy 3 months ago - 10 comments

#150 - Images not appearing in registered slide directory

Issue - State: closed - Opened by snackthingy 3 months ago - 6 comments

#149 - Error

Issue - State: closed - Opened by snackthingy 3 months ago - 5 comments

#148 - new dockerfile

Pull Request - State: open - Opened by Gibbsdavidl 3 months ago

#147 - Passing a rigid transformation to the registrar

Issue - State: open - Opened by pauldoucet 4 months ago - 3 comments

#146 - UnboundLocalError: cannot access local variable 'slide_dimensions' where it is not associated with a value

Issue - State: closed - Opened by SinaSOX 4 months ago - 1 comment

#145 - Running the code on kaggle

Issue - State: open - Opened by SinaSOX 4 months ago
Labels: question

#144 - What is the best platform(or linux distribution) to run the code?

Issue - State: closed - Opened by SinaSOX 4 months ago

#143 - Not producing output

Issue - State: open - Opened by dr-sayyadhury 4 months ago - 4 comments

#142 - very large ome.tiff file size

Issue - State: closed - Opened by minajamshidi 4 months ago - 3 comments
Labels: question

#141 - Non-Rigid Registration Error

Issue - State: open - Opened by ewestlundicr 5 months ago - 11 comments

#140 - Non Rigid registration

Issue - State: open - Opened by simomounir 5 months ago - 1 comment
Labels: question

#139 - OSError cannot load library 'libvips.so.42' on the latest Docker image

Issue - State: open - Opened by KOBE24DUNK 5 months ago - 4 comments

#138 - IndexError: list index out of range

Issue - State: closed - Opened by KOBE24DUNK 5 months ago - 5 comments

#137 - Only DAPI image when merging, with feedback "Have already added all channels in ['DAPI']"

Issue - State: closed - Opened by KOBE24DUNK 5 months ago

#136 - Error with registration when I use a cropped version of the image

Issue - State: open - Opened by msberges 5 months ago - 2 comments

#133 - register 3d images (X,Y,Z) and register from various objectives (x20 /x63) ?

Issue - State: open - Opened by Nal44 5 months ago - 9 comments

#132 - Register DAPI image and IHC image (rgb) ?

Issue - State: closed - Opened by Nal44 5 months ago - 5 comments

#131 - Unexpected colored pixels after registration

Issue - State: open - Opened by kevin346-sc 6 months ago - 1 comment

#130 - valis requires and outdated version of pydantic through ome-types

Issue - State: closed - Opened by iRyoka 6 months ago - 2 comments

#129 - Micron/Pixel for best registration results

Issue - State: open - Opened by lifangda01 6 months ago

#128 - Where to choose the default GPU

Issue - State: open - Opened by syy-create 6 months ago - 2 comments

#127 - Warping cell and transcript x,y coordinates - unable to shift or warp

Issue - State: open - Opened by dr-sayyadhury 6 months ago - 1 comment
Labels: stale

#126 - Transfer annotations from one image to other previously registered.

Issue - State: closed - Opened by msberges 6 months ago - 3 comments

#125 - Batch registration and merge of multiplexed images + Whole Slide Processing slicing

Issue - State: open - Opened by andreevg04 7 months ago - 3 comments

#124 - large tiff output

Issue - State: closed - Opened by lingxitong 7 months ago - 2 comments
Labels: question

#123 - Merging channels and not getting the first image I want to get the DAPI from

Issue - State: open - Opened by andreevg04 7 months ago - 7 comments

#122 - ann transfer

Issue - State: closed - Opened by lingxitong 7 months ago - 18 comments

#121 - add new wsi .format?

Issue - State: open - Opened by lingxitong 7 months ago - 3 comments
Labels: question

#120 - How to register at a specific magnification

Issue - State: open - Opened by syy-create 7 months ago

#118 - Problems with tiled non-rigid registration

Issue - State: open - Opened by batukav 7 months ago - 3 comments

#117 - How to read data from non-standard slide libraries

Issue - State: closed - Opened by syy-create 8 months ago - 1 comment

#116 - Will Valis work under Centos 7?

Issue - State: open - Opened by yaoxiaoxu0630 8 months ago - 3 comments

#115 - adding sched_getaffinity when available to determine number of procs

Pull Request - State: closed - Opened by p-smirnov 8 months ago - 1 comment

#114 - Enhancement: respecting cgroup cpu limits

Issue - State: closed - Opened by p-smirnov 8 months ago - 1 comment

#113 - check_flattened_pyramid_tiff question

Issue - State: open - Opened by p-smirnov 8 months ago - 3 comments

#112 - Installation/import problem -- 'xfeatures2d module is not available'

Issue - State: open - Opened by stevenjayfrank 8 months ago - 7 comments

#110 - TypeError:'NoneType' object is not subscriptable

Issue - State: closed - Opened by syy-create 8 months ago - 15 comments

#109 - slide level save

Issue - State: open - Opened by lingxitong 8 months ago - 2 comments

#108 - Why the inverse matrix in warp_tools.warp_xy_rigid?

Issue - State: closed - Opened by lifangda01 8 months ago - 1 comment
Labels: question

#107 - That is the difference between "towards" and "directly to"?

Issue - State: closed - Opened by ciaobladoo 9 months ago - 5 comments
Labels: question

#106 - Which registered version is saved?

Issue - State: open - Opened by ciaobladoo 9 months ago - 7 comments
Labels: question

#105 - Issues with large image stack alignment

Issue - State: open - Opened by pgensbigler 9 months ago - 2 comments

#104 - Key Error encountered during Rigid Registration

Issue - State: open - Opened by ciaobladoo 9 months ago - 2 comments

#103 - Radians instead of degrees in np.sin() and np.cos()?

Issue - State: closed - Opened by lifangda01 10 months ago - 2 comments

#102 - ValueError: cannot convert float NaN to integer

Issue - State: closed - Opened by ciaobladoo 10 months ago - 3 comments

#101 - File size and channel names

Issue - State: open - Opened by smith6jt-cop 10 months ago - 10 comments

#100 - UnboundLocalError: local variable 'slide_obj' referenced before assignment

Issue - State: closed - Opened by ciaobladoo 10 months ago - 4 comments

#96 - list index out of range

Issue - State: open - Opened by dr-sayyadhury 10 months ago - 5 comments

#95 - Fixed error estimate in reflection detection in serial_rigid.py

Pull Request - State: closed - Opened by lifangda01 10 months ago - 1 comment

#94 - ValueError: array to be byte-swapped is read-only

Issue - State: closed - Opened by smith6jt-cop 10 months ago - 5 comments

#93 - UnboundLocalError: local variable 'slide_dimensions' referenced before assignment

Issue - State: open - Opened by melanieloth 10 months ago - 2 comments

#92 - Encountering difficulties installing valis-wsi due to compatibility issues with Python 3.12.

Issue - State: open - Opened by jeginderof 10 months ago - 2 comments

#91 - Channels merged during merging registered CyCIF images

Issue - State: closed - Opened by Ajaingithub 11 months ago - 1 comment

#90 - Issue saving the ome.tiff while merging 2channel tiffs.

Issue - State: open - Opened by andreevg04 11 months ago - 13 comments

#89 - list index out of range error when trying to save registered slides

Issue - State: closed - Opened by ciaobladoo 11 months ago - 12 comments

#88 - Saving as SVS file?

Issue - State: closed - Opened by ciaobladoo 11 months ago - 2 comments

#87 - valis == 1.0.2 error

Issue - State: closed - Opened by 464hee 11 months ago

#86 - registrar.warp_and_save_slides function not producing output

Issue - State: open - Opened by melanieloth 12 months ago - 10 comments

#85 - acrobat_2023 registration

Issue - State: open - Opened by aliuak about 1 year ago - 1 comment
Labels: stale

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

Issue - State: open - Opened by daviddaiweizhang about 1 year ago - 16 comments

#82 - Tiff Write Error

Issue - State: open - Opened by Justin-Krieg about 1 year ago

#81 - Works with Lif file Or Tiff files as a source ?

Issue - State: open - Opened by Nal44 about 1 year ago - 38 comments

#80 - TurboJPEG error?

Issue - State: closed - Opened by billnjcn111 about 1 year ago - 12 comments

#79 - non-rigid registration

Issue - State: closed - Opened by cristinaperez9 about 1 year ago - 1 comment

#78 - KeyError: 'None' error while using warp_and_save_slide to save ome.tiff

Issue - State: open - Opened by arundasan91 about 1 year ago - 14 comments

#77 - Apply registration to new image does not work using the warp_slide function.

Issue - State: closed - Opened by linchundan88 about 1 year ago - 1 comment

#76 - 'NoneType' object has no attribute 'shape'

Issue - State: open - Opened by Justin-Krieg about 1 year ago - 19 comments

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

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

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

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

#73 - after registration, parameters for rigid registration

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

#72 - Increased epsilon value in norm_img_stats

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

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

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

#70 - Rigid registration attempts impossible warps

Issue - State: open - Opened by dnschouten about 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 - 23 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

GitHub / MathOnco/valis issues and pull requests