Fixes contained in non-main branches

[tstoeger]

As requested an overview of recent fixes and their status:

get_image_snake Support for microscope slides ("wells" with ~1000 sites). This code has run on iBrain via LIB without problems on ~10 plates of mine. Update of the code is minor and only triggered in case where currently deployed version would cause error and break. In addition to the existing unit test, I added a unit test for the extension of the heuristics. Update is part of the non-main branch https://github.com/pelkmanslab/iBRAINShared/tree/TScurrentlyDeveloppingSupportForSlides . Also see https://github.com/pelkmanslab/iBRAIN_BRUTUS/issues/22

stitchSegmentationPerWell Support for microscope slides ("wells" with ~1000 sites). This code has run on iBrain via LIB without problems on ~10 plates of mine (and I tested compatibility of this output with standard function for projecting data on cell segmentations). Update of the code is relatively large and includes alterations of lines, which are also called for wells with less sites, where they however should not interfere with the output. All changes in the update of the module anticipate situations where the stitched well segmentation, which is saved as a png image, exceeds the maximal dimensions of a png image (which would cause error in presently deployed version). a) Only in situations, where the output would not be able to be generated, the output image is downsampled without interpolation. b) The downsampling is however already done at the level of the import of the individual segmentation-images (rather than immediately prior to saving) to avoid out-of-memory (I did not test the specific memory requirement, but jobs kept crashin on iBrain/Brutus providing ~15GB). Since there was not yet any unit test for the currently deployed version, I did not add an additional unit test for the fix. Update is part of the non-main branch https://github.com/pelkmanslab/iBRAINShared/tree/TScurrentlyDeveloppingSupportForSlides . Also see https://github.com/pelkmanslab/iBRAIN_BRUTUS/issues/23

check_image_channel Support for CV7K's nomenclature for acquisitions with >999 sites. The deployed fix has been working perfectly ( see closed issue https://github.com/pelkmanslab/PelkmansLibrary/issues/6 ). To prevent excessive branches in the repository, I'd suggest to remove the branch https://github.com/pelkmanslab/PelkmansLibrary/tree/SupportSlidesFromCv7k as it is no longer needed.

npc Support for share 9 and share 10. The update is very small and appears very safe and consists of a) adding the names of share 9 and 10 and b) allowing share numbers to have two digits. The update has not been tested on iBrain (locally on Windows it works). There is no unit test for the presently deployed version of npc and I did not design a test for the update. Update is in non-main branch https://github.com/pelkmanslab/PelkmansLibrary/tree/extendedNPc , which could be deleted upon the merge request https://github.com/pelkmanslab/PelkmansLibrary/pull/9

minor fixes in CP modules all contained in https://github.com/pelkmanslab/CellProfilerPelkmans/tree/newModulesAlreadyTestedOnIBrain

IdentifySecondaryIterative Only relates to GUI (and thus local machine). Design problem, which prevents seeing the outline on the image, if few cells are present (e.g.: on micropatterned cover slips): now improved contrast and outline shown in red instead of same color as image data

SourceExtractorDeblend add forgotten line break to avoid concatenation of output

[ewiger]

Thomas thank you for this summary. This will help to test and merge changes (a lot!).

[tstoeger]

just closing issues that I opened in Github, but which in the meantime are solved