Ecosyste.ms: Issues

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GitHub / MathOnco/valis issues and pull requests

#183 - Slow processing of OME-TIFF images

Issue - State: open - Opened by njspix 8 days ago

#181 - Valis rigid registration error

Issue - State: open - Opened by 171909771 10 days ago - 1 comment

#180 - Vulnerability in pillow

Issue - State: open - Opened by j0d0nn about 2 months ago - 1 comment

#179 - bad effect

Issue - State: open - Opened by wanglala6 about 2 months ago

#178 - fix #176, librsvg-2.so.2 not found

Pull Request - State: open - Opened by huboqiang about 2 months ago

#177 - Strange color in generated ome.tiff

Issue - State: closed - Opened by pimooook about 2 months ago

#176 - Wrong 1.1.0 docker image

Issue - State: open - Opened by huboqiang about 2 months ago - 2 comments

#175 - Totally wrong with roi mask detection

Issue - State: closed - Opened by pimooook about 2 months ago - 3 comments

#174 - What is "register.py" in docker command?

Issue - State: closed - Opened by pimooook about 2 months ago - 1 comment

#173 - Assertion Error transfering geojson annotations

Issue - State: open - Opened by marcosgly about 2 months ago - 2 comments

#172 - How is keypoint detection specified as a Superpoint method？

Issue - State: open - Opened by zhahaha123 2 months ago - 2 comments

#170 - bug: Sometimes "reference_img_f" is ignored.

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

#169 - Don't see stacked images saved as OME-TIFF

Issue - State: closed - Opened by WillYe45 3 months ago - 5 comments

#166 - Bug when warping and merging?

Issue - State: open - Opened by simomounir 4 months ago - 1 comment

#164 - Unable to read .qptiff files

Issue - State: open - Opened by Wenke-Liu 4 months ago - 2 comments

#162 - facing error using NonRigidRegistrarGroupwise

Issue - State: open - Opened by shubhankar-git 5 months ago

#161 - error using SimpleElastixWarper

Issue - State: open - Opened by shubhankar-git 5 months ago

#160 - Issues with points - not transformed correctly?

Issue - State: open - Opened by lukasz-migas 5 months ago - 5 comments

#159 - Zen 3.8+ Incompatibility

Issue - State: open - Opened by Justin-Krieg 5 months ago - 1 comment

#158 - Docker usage generates nonsensical image

Issue - State: closed - Opened by Justin-Krieg 5 months ago - 1 comment

#157 - register problem

Issue - State: open - Opened by lingxitong 5 months ago - 1 comment

#156 - Specify Channel Order When Merging

Issue - State: closed - Opened by ewestlundicr 5 months ago - 2 comments
Labels: question

#155 - Save only one Tiff

Issue - State: closed - Opened by lingxitong 5 months ago - 4 comments

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

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

#153 - Processing Images with Low Brightness and Contrast

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

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

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

#151 - Saving as .ome.tiff

Issue - State: open - Opened by snackthingy 6 months ago - 10 comments

#150 - Images not appearing in registered slide directory

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

#149 - Error

Issue - State: closed - Opened by snackthingy 6 months ago - 5 comments

#148 - new dockerfile

Pull Request - State: closed - Opened by Gibbsdavidl 6 months ago

#147 - Passing a rigid transformation to the registrar

Issue - State: open - Opened by pauldoucet 6 months ago - 3 comments

#145 - Running the code on kaggle

Issue - State: open - Opened by SinaSOX 6 months ago
Labels: question

#143 - Not producing output

Issue - State: open - Opened by dr-sayyadhury 7 months ago - 4 comments

#142 - very large ome.tiff file size

Issue - State: closed - Opened by minajamshidi 7 months ago - 3 comments
Labels: question

#141 - Non-Rigid Registration Error

Issue - State: open - Opened by ewestlundicr 7 months ago - 11 comments

#140 - Non Rigid registration

Issue - State: open - Opened by simomounir 7 months ago - 1 comment
Labels: question

#138 - IndexError: list index out of range

Issue - State: closed - Opened by KOBE24DUNK 7 months ago - 5 comments

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

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

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

Issue - State: closed - Opened by Nal44 8 months ago - 5 comments

#131 - Unexpected colored pixels after registration

Issue - State: open - Opened by kevin346-sc 8 months ago - 1 comment

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

Issue - State: closed - Opened by iRyoka 8 months ago - 2 comments

#129 - Micron/Pixel for best registration results

Issue - State: open - Opened by lifangda01 9 months ago

#128 - Where to choose the default GPU

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

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

Issue - State: open - Opened by dr-sayyadhury 9 months ago - 1 comment
Labels: stale

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

Issue - State: closed - Opened by msberges 9 months ago - 3 comments

#124 - large tiff output

Issue - State: closed - Opened by lingxitong 9 months ago - 2 comments
Labels: question

#122 - ann transfer

Issue - State: closed - Opened by lingxitong 9 months ago - 18 comments

#121 - add new wsi .format?

Issue - State: open - Opened by lingxitong 9 months ago - 3 comments
Labels: question

#120 - How to register at a specific magnification

Issue - State: open - Opened by syy-create 10 months ago

#118 - Problems with tiled non-rigid registration

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

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

Issue - State: closed - Opened by syy-create 10 months ago - 1 comment

#116 - Will Valis work under Centos 7?

Issue - State: open - Opened by yaoxiaoxu0630 10 months ago - 3 comments

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

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

#114 - Enhancement: respecting cgroup cpu limits

Issue - State: closed - Opened by p-smirnov 10 months ago - 1 comment

#113 - check_flattened_pyramid_tiff question

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

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

Issue - State: closed - Opened by syy-create 10 months ago - 15 comments

#109 - slide level save

Issue - State: open - Opened by lingxitong 11 months ago - 2 comments

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

Issue - State: closed - Opened by lifangda01 11 months ago - 1 comment
Labels: question

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

Issue - State: closed - Opened by ciaobladoo 11 months ago - 5 comments
Labels: question

#106 - Which registered version is saved?

Issue - State: open - Opened by ciaobladoo 11 months ago - 7 comments
Labels: question

#105 - Issues with large image stack alignment

Issue - State: open - Opened by pgensbigler 11 months ago - 2 comments

#104 - Key Error encountered during Rigid Registration

Issue - State: open - Opened by ciaobladoo 12 months ago - 2 comments

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

Issue - State: closed - Opened by lifangda01 12 months ago - 2 comments

#102 - ValueError: cannot convert float NaN to integer

Issue - State: closed - Opened by ciaobladoo 12 months ago - 3 comments

#101 - File size and channel names

Issue - State: open - Opened by smith6jt-cop about 1 year ago - 10 comments

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

Issue - State: closed - Opened by ciaobladoo about 1 year ago - 4 comments

#96 - list index out of range

Issue - State: open - Opened by dr-sayyadhury about 1 year ago - 5 comments

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

Pull Request - State: closed - Opened by lifangda01 about 1 year ago - 1 comment

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

Issue - State: closed - Opened by smith6jt-cop about 1 year ago - 5 comments

#91 - Channels merged during merging registered CyCIF images

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

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

Issue - State: open - Opened by andreevg04 about 1 year ago - 13 comments

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

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

#88 - Saving as SVS file?

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

#87 - valis == 1.0.2 error

Issue - State: closed - Opened by 464hee about 1 year ago

#86 - registrar.warp_and_save_slides function not producing output

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

#80 - TurboJPEG error?

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

#79 - non-rigid registration

Issue - State: closed - Opened by cristinaperez9 over 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 over 1 year ago - 14 comments

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

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