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Injectionsite #19
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Injectionsite #19
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adamltyson
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Apr 16, 2020
* points to brainrender * update testing * refactor * refactor * badges * notes * initial inj finder commit (#11) * formatting with black * add .DS_store to gitignore * typo * update imports * update imports * deal with no obj path given * error typo * move utils too imlib * remove amap imports * optional logging to file * tidy * registration moved to imlib * keep largest object * reduce RAM usage * remove unnecessary logging args * adds lesion and track estimation and generic tools * add missing dir support for cell export * add missing dir support for cell export * reduce mem requirements * remove old code * remove old code * refactor scaling * fix failing heatmap test * update docs * ensure output directory exists * make pixel sizes mandatory * make pixel sizes mandatory (#17) * move functionality to imlib * remove hard coded smoothing * Refactor (#19) * make pixel sizes mandatory * move functionality to imlib * remove hard coded smoothing * update docs * Injectionsite (#20) * refactors code from SL to import from neuro and imlib only * moves amap_vis to neuro and removes amap and cellfinder dependencies; * format with black * amap_vis Co-authored-by: Federico Claudi <federicoclaudi@protonmail.com> Co-authored-by: stephen <stephen.lenzi@gmail.com>
adamltyson
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Apr 17, 2020
* points to brainrender * update testing * refactor * refactor * badges * notes * initial inj finder commit (#11) * formatting with black * add .DS_store to gitignore * typo * update imports * update imports * deal with no obj path given * error typo * move utils too imlib * remove amap imports * optional logging to file * tidy * registration moved to imlib * keep largest object * reduce RAM usage * remove unnecessary logging args * adds lesion and track estimation and generic tools * add missing dir support for cell export * add missing dir support for cell export * reduce mem requirements * remove old code * remove old code * refactor scaling * fix failing heatmap test * update docs * ensure output directory exists * make pixel sizes mandatory * make pixel sizes mandatory (#17) * move functionality to imlib * remove hard coded smoothing * Refactor (#19) * make pixel sizes mandatory * move functionality to imlib * remove hard coded smoothing * update docs * Injectionsite (#20) * refactors code from SL to import from neuro and imlib only * moves amap_vis to neuro and removes amap and cellfinder dependencies; * format with black * amap_vis * bump * remove cellfinder dependency * cli entry point for fibre track segmentation * refactor seg tools * start manual seg * remove hardocoding in manual region segmentation * refactor paths * bump Co-authored-by: Federico Claudi <federicoclaudi@protonmail.com> Co-authored-by: stephen <stephen.lenzi@gmail.com>
adamltyson
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Apr 20, 2020
* points to brainrender * update testing * refactor * refactor * badges * notes * initial inj finder commit (#11) * formatting with black * add .DS_store to gitignore * typo * update imports * update imports * deal with no obj path given * error typo * move utils too imlib * remove amap imports * optional logging to file * tidy * registration moved to imlib * keep largest object * reduce RAM usage * remove unnecessary logging args * adds lesion and track estimation and generic tools * add missing dir support for cell export * add missing dir support for cell export * reduce mem requirements * remove old code * remove old code * refactor scaling * fix failing heatmap test * update docs * ensure output directory exists * make pixel sizes mandatory * make pixel sizes mandatory (#17) * move functionality to imlib * remove hard coded smoothing * Refactor (#19) * make pixel sizes mandatory * move functionality to imlib * remove hard coded smoothing * update docs * Injectionsite (#20) * refactors code from SL to import from neuro and imlib only * moves amap_vis to neuro and removes amap and cellfinder dependencies; * format with black * amap_vis * bump * remove cellfinder dependency * cli entry point for fibre track segmentation * refactor seg tools * start manual seg * remove hardocoding in manual region segmentation * refactor paths * bump * update docs * update docs * update docs * update docs * support multiple objects * color objects * bump * update reqs Co-authored-by: Federico Claudi <federicoclaudi@protonmail.com> Co-authored-by: stephen <stephen.lenzi@gmail.com>
adamltyson
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Apr 22, 2020
* points to brainrender * update testing * refactor * refactor * badges * notes * initial inj finder commit (#11) * formatting with black * add .DS_store to gitignore * typo * update imports * update imports * deal with no obj path given * error typo * move utils too imlib * remove amap imports * optional logging to file * tidy * registration moved to imlib * keep largest object * reduce RAM usage * remove unnecessary logging args * adds lesion and track estimation and generic tools * add missing dir support for cell export * add missing dir support for cell export * reduce mem requirements * remove old code * remove old code * refactor scaling * fix failing heatmap test * update docs * ensure output directory exists * make pixel sizes mandatory * make pixel sizes mandatory (#17) * move functionality to imlib * remove hard coded smoothing * Refactor (#19) * make pixel sizes mandatory * move functionality to imlib * remove hard coded smoothing * update docs * Injectionsite (#20) * refactors code from SL to import from neuro and imlib only * moves amap_vis to neuro and removes amap and cellfinder dependencies; * format with black * amap_vis * bump * remove cellfinder dependency * cli entry point for fibre track segmentation * refactor seg tools * start manual seg * remove hardocoding in manual region segmentation * refactor paths * bump * update docs * update docs * update docs * update docs * support multiple objects * color objects * bump * update reqs * improve rendering of flat objects * bump * prevent saving unnecessary common volume * allow ROIs to be edited * label regions * bump * bump Co-authored-by: Federico Claudi <federicoclaudi@protonmail.com> Co-authored-by: stephen <stephen.lenzi@gmail.com>
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