Issues

• CellposeSAM segmentation doubles the dimensions of the masks

  BodenmillerGroup/steinbock#291 · Filter by author JohnAbbey98 opened on May 4, 2026
  3

• behavior in measure intensities

  BodenmillerGroup/steinbock#288 · Filter by author SchulzDan opened on Mar 27, 2026
  2

• Fibroblast Cells Missed

  BodenmillerGroup/steinbock#285 · Filter by author DarioS opened on Aug 6, 2025

• inconsistent image acquisition error causes empty images.csv

  BodenmillerGroup/steinbock#284 · Filter by author matt-sd-watson opened on Aug 1, 2025

• Some problem when running ilastik fix（KeyError: 'Patient1_s0_a1_ac_ilastik_x593_y590_w500_h500'）

  BodenmillerGroup/steinbock#283 · Filter by author yibulaxin opened on Jul 31, 2025
  1

• MCD Directory Checked Even if Only TXT Path Specified

  BodenmillerGroup/steinbock#282 · Filter by author DarioS opened on Jul 25, 2025
  2

• MCD files generated with the slide loader always appear corrupted

  BodenmillerGroup/steinbock#281 · Filter by author givison opened on Apr 15, 2025
  2

• Having difficulty to do segmentation with external images

  BodenmillerGroup/steinbock#279 · Filter by author xwxdazhong opened on Mar 14, 2025
  1

• [Errno 2] No such file or directory: '/opt/ilastik/run_ilastik.sh'

  BodenmillerGroup/steinbock#278 · Filter by author mdka00001 opened on Mar 5, 2025
  1

• Auto detect if imwrite should use ome and bigtiff or not

  BodenmillerGroup/steinbock#275 · Filter by author matt-sd-watson opened on Dec 13, 2024
  2

• Docker container keeps exiting

  BodenmillerGroup/steinbock#274 · Filter by author SamWell16 opened on Dec 11, 2024

• Set mask dtype to np.uint32 by default without using ENV variables?

  BodenmillerGroup/steinbock#272 · Filter by author matt-sd-watson opened on Nov 20, 2024
  3

• Command "preprocess imc images" generate tiff file with only image for one channel

  BodenmillerGroup/steinbock#271 · Filter by author xwxdazhong opened on Nov 15, 2024
  1

• Strange invalid literal error..

  bug
  BodenmillerGroup/steinbock#259 · Filter by author paulrbuckley-kcl opened on May 9, 2024
  2

• [Bug]No neighborhood Data in h5ad-files?

  duplicate
  BodenmillerGroup/steinbock#210 · Filter by author albert180 opened on Aug 9, 2023
  1

• tissuenet model support and documentation

  documentation
  BodenmillerGroup/steinbock#208 · Filter by author lassedochreden opened on Aug 3, 2023
  1

• Maximum amount of segmented cells bounded from segmentation output file format (16-bit unsigned integer TIFF images)

  documentation
  BodenmillerGroup/steinbock#207 · Filter by author asom opened on Aug 2, 2023
  4

• Using the preprocess external option with large images

  bug
  BodenmillerGroup/steinbock#206 · Filter by author mjseignon opened on Jul 17, 2023
  6

• cytomarker panels

  enhancement
  BodenmillerGroup/steinbock#205 · Filter by author jwindhager opened on Jul 11, 2023

• Add option to remove the first acquisition row in IMC images.

  enhancement
  BodenmillerGroup/steinbock#204 · Filter by author nathansteenbuck opened on Jul 11, 2023
  1

• --strict/--no-strict for steinbock preprocess imc images command

  enhancement
  BodenmillerGroup/steinbock#202 · Filter by author jwindhager opened on Jun 30, 2023

• TypeError - code that used to work

  BodenmillerGroup/steinbock#201 · Filter by author paulrbuckley-kcl opened on Jun 28, 2023

• Add a --channels-last option to steinbock preprocess external

  enhancement
  BodenmillerGroup/steinbock#199 · Filter by author jwindhager opened on Jun 21, 2023

• Obfuscated logging in external preprocessing

  bug
  BodenmillerGroup/steinbock#198 · Filter by author jwindhager opened on Jun 20, 2023

• ome-tiff issue

  BodenmillerGroup/steinbock#197 · Filter by author paulrbuckley-kcl opened on Jun 20, 2023
  3