Changelog
[v0.12.0](https://github.com/ABI-Software/scaffoldmaker/tree/v0.12.0) (2024-04-05)
[Full Changelog](https://github.com/ABI-Software/scaffoldmaker/compare/v0.11.0...v0.12.0)
**Merged pull requests:**
- Limit bifurcation trim surface intersections to half curve [\247](https://github.com/ABI-Software/scaffoldmaker/pull/247) ([rchristie](https://github.com/rchristie))
- Box network [\246](https://github.com/ABI-Software/scaffoldmaker/pull/246) ([rchristie](https://github.com/rchristie))
- Implement straight-through bifurcation case [\242](https://github.com/ABI-Software/scaffoldmaker/pull/242) ([rchristie](https://github.com/rchristie))
- Smooth side derivatives and inner coordinates [\241](https://github.com/ABI-Software/scaffoldmaker/pull/241) ([rchristie](https://github.com/rchristie))
- Network tube [\240](https://github.com/ABI-Software/scaffoldmaker/pull/240) ([rchristie](https://github.com/rchristie))
- initial commit of bone scaffold [\239](https://github.com/ABI-Software/scaffoldmaker/pull/239) ([vickieshim](https://github.com/vickieshim))
- Cecum new [\234](https://github.com/ABI-Software/scaffoldmaker/pull/234) ([mlin865](https://github.com/mlin865))
[v0.11.0](https://github.com/ABI-Software/scaffoldmaker/tree/v0.11.0) (2023-09-22)
[Full Changelog](https://github.com/ABI-Software/scaffoldmaker/compare/v0.10.0...v0.11.0)
**Closed issues:**
- Bladder 1 issues [\228](https://github.com/ABI-Software/scaffoldmaker/issues/228)
**Merged pull requests:**
- Test uterus network [\238](https://github.com/ABI-Software/scaffoldmaker/pull/238) ([zekh167](https://github.com/zekh167))
- Handle d1 scaling when using inward and update unit test for bladder [\237](https://github.com/ABI-Software/scaffoldmaker/pull/237) ([mlin865](https://github.com/mlin865))
- Stomach [\236](https://github.com/ABI-Software/scaffoldmaker/pull/236) ([mlin865](https://github.com/mlin865))
- Bladder coordinates [\235](https://github.com/ABI-Software/scaffoldmaker/pull/235) ([zekh167](https://github.com/zekh167))
- Biunit bladder [\233](https://github.com/ABI-Software/scaffoldmaker/pull/233) ([rchristie](https://github.com/rchristie))
- Modified bladder [\231](https://github.com/ABI-Software/scaffoldmaker/pull/231) ([zekh167](https://github.com/zekh167))
[v0.10.0](https://github.com/ABI-Software/scaffoldmaker/tree/v0.10.0) (2023-07-19)
[Full Changelog](https://github.com/ABI-Software/scaffoldmaker/compare/v0.9.0...v0.10.0)
**Fixed bugs:**
- Derivative smoothing incorrect for single element branches using versions [\224](https://github.com/ABI-Software/scaffoldmaker/issues/224)
**Merged pull requests:**
- Zohreh new bladder [\229](https://github.com/ABI-Software/scaffoldmaker/pull/229) ([rchristie](https://github.com/rchristie))
- Apply zinc group changes [\226](https://github.com/ABI-Software/scaffoldmaker/pull/226) ([rchristie](https://github.com/rchristie))
- Intestines [\225](https://github.com/ABI-Software/scaffoldmaker/pull/225) ([mlin865](https://github.com/mlin865))
- Network mesh [\223](https://github.com/ABI-Software/scaffoldmaker/pull/223) ([rchristie](https://github.com/rchristie))
- Decode JSON containing sub-scaffoldPackages [\222](https://github.com/ABI-Software/scaffoldmaker/pull/222) ([Kayvv](https://github.com/Kayvv))
[v0.9.0](https://github.com/ABI-Software/scaffoldmaker/tree/v0.9.0) (2023-04-17)
[Full Changelog](https://github.com/ABI-Software/scaffoldmaker/compare/v0.8.0...v0.9.0)
**Merged pull requests:**
- Rename to CMLibs [\221](https://github.com/ABI-Software/scaffoldmaker/pull/221) ([hsorby](https://github.com/hsorby))
- Fix group field utility to work with region tree [\220](https://github.com/ABI-Software/scaffoldmaker/pull/220) ([rchristie](https://github.com/rchristie))
[v0.8.0](https://github.com/ABI-Software/scaffoldmaker/tree/v0.8.0) (2022-11-21)
[Full Changelog](https://github.com/ABI-Software/scaffoldmaker/compare/v0.7.1...v0.8.0)
**Implemented enhancements:**
- Marker points need separate material coordinates field [\217](https://github.com/ABI-Software/scaffoldmaker/issues/217)
- Marker node annotations should not make zinc groups [\215](https://github.com/ABI-Software/scaffoldmaker/issues/215)
**Merged pull requests:**
- Update docs to list where data for scaffold came from [\218](https://github.com/ABI-Software/scaffoldmaker/pull/218) ([mlin865](https://github.com/mlin865))
- Marker point annotations do not have their own group [\216](https://github.com/ABI-Software/scaffoldmaker/pull/216) ([rchristie](https://github.com/rchristie))
- Nerves/material coordinates [\214](https://github.com/ABI-Software/scaffoldmaker/pull/214) ([elias-soltani](https://github.com/elias-soltani))
- Unit stomach [\213](https://github.com/ABI-Software/scaffoldmaker/pull/213) ([mlin865](https://github.com/mlin865))
- Adjust range of elements according to updated number of elements. [\179](https://github.com/ABI-Software/scaffoldmaker/pull/179) ([elias-soltani](https://github.com/elias-soltani))
[v0.7.1](https://github.com/ABI-Software/scaffoldmaker/tree/v0.7.1) (2022-09-03)
[Full Changelog](https://github.com/ABI-Software/scaffoldmaker/compare/v0.7.0...v0.7.1)
**Fixed bugs:**
- Deleting any elements deletes any new style marker points without material coordinates [\211](https://github.com/ABI-Software/scaffoldmaker/issues/211)
**Closed issues:**
- Documentation on generating new scaffolds [\182](https://github.com/ABI-Software/scaffoldmaker/issues/182)
**Merged pull requests:**
- Fix logic for removing marker nodes when elements deleted [\212](https://github.com/ABI-Software/scaffoldmaker/pull/212) ([rchristie](https://github.com/rchristie))
- Bladder documentation [\210](https://github.com/ABI-Software/scaffoldmaker/pull/210) ([zekh167](https://github.com/zekh167))
- Scaffold documentation for stomach and colon [\204](https://github.com/ABI-Software/scaffoldmaker/pull/204) ([mlin865](https://github.com/mlin865))
[v0.7.0](https://github.com/ABI-Software/scaffoldmaker/tree/v0.7.0) (2022-08-25)
[Full Changelog](https://github.com/ABI-Software/scaffoldmaker/compare/v0.6.0...v0.7.0)
**Merged pull requests:**
- Marker points [\208](https://github.com/ABI-Software/scaffoldmaker/pull/208) ([mlin865](https://github.com/mlin865))
[v0.6.0](https://github.com/ABI-Software/scaffoldmaker/tree/v0.6.0) (2022-08-08)
[Full Changelog](https://github.com/ABI-Software/scaffoldmaker/compare/v0.5.0...v0.6.0)
**Merged pull requests:**
- Move stomach changes to new branch [\203](https://github.com/ABI-Software/scaffoldmaker/pull/203) ([mlin865](https://github.com/mlin865))
- Improve brainstem and lung scaffold documentation [\202](https://github.com/ABI-Software/scaffoldmaker/pull/202) ([rchristie](https://github.com/rchristie))
- Add docs for brainstem and lung [\199](https://github.com/ABI-Software/scaffoldmaker/pull/199) ([arti-sukasem](https://github.com/arti-sukasem))
- Flat bladder [\186](https://github.com/ABI-Software/scaffoldmaker/pull/186) ([zekh167](https://github.com/zekh167))
[v0.5.0](https://github.com/ABI-Software/scaffoldmaker/tree/v0.5.0) (2022-07-26)
[Full Changelog](https://github.com/ABI-Software/scaffoldmaker/compare/v0.4.4...v0.5.0)
**Merged pull requests:**
- Lung 2 scaffold [\200](https://github.com/ABI-Software/scaffoldmaker/pull/200) ([rchristie](https://github.com/rchristie))
- Update heart terms, improve epicardium, add docs [\195](https://github.com/ABI-Software/scaffoldmaker/pull/195) ([rchristie](https://github.com/rchristie))
- Add basis for documentation [\190](https://github.com/ABI-Software/scaffoldmaker/pull/190) ([hsorby](https://github.com/hsorby))
- Add epicardial fat layer to atrium [\187](https://github.com/ABI-Software/scaffoldmaker/pull/187) ([rchristie](https://github.com/rchristie))
- Add fusiform muscle [\180](https://github.com/ABI-Software/scaffoldmaker/pull/180) ([elias-soltani](https://github.com/elias-soltani))
[v0.4.4](https://github.com/ABI-Software/scaffoldmaker/tree/v0.4.4) (2022-04-22)
[Full Changelog](https://github.com/ABI-Software/scaffoldmaker/compare/v0.4.3...v0.4.4)
**Merged pull requests:**
- Add user marker point annotation groups [\184](https://github.com/ABI-Software/scaffoldmaker/pull/184) ([rchristie](https://github.com/rchristie))
[v0.4.3](https://github.com/ABI-Software/scaffoldmaker/tree/v0.4.3) (2022-03-22)
[Full Changelog](https://github.com/ABI-Software/scaffoldmaker/compare/v0.4.2...v0.4.3)
[v0.4.2](https://github.com/ABI-Software/scaffoldmaker/tree/v0.4.2) (2022-03-21)
[Full Changelog](https://github.com/ABI-Software/scaffoldmaker/compare/v0.4.1...v0.4.2)
**Merged pull requests:**
- Update esophagus terms after term addition to sciCrunch [\183](https://github.com/ABI-Software/scaffoldmaker/pull/183) ([mlin865](https://github.com/mlin865))
[v0.4.1](https://github.com/ABI-Software/scaffoldmaker/tree/v0.4.1) (2022-03-15)
[Full Changelog](https://github.com/ABI-Software/scaffoldmaker/compare/v0.4.0...v0.4.1)
**Closed issues:**
- Basic info on starting with scaffoldmaker [\181](https://github.com/ABI-Software/scaffoldmaker/issues/181)
[v0.4.0](https://github.com/ABI-Software/scaffoldmaker/tree/v0.4.0) (2022-03-10)
[Full Changelog](https://github.com/ABI-Software/scaffoldmaker/compare/v0.3.0...v0.4.0)
**Merged pull requests:**
- Add meshtype, terms and unit test for esophagus [\178](https://github.com/ABI-Software/scaffoldmaker/pull/178) ([mlin865](https://github.com/mlin865))
- Pig stomach [\177](https://github.com/ABI-Software/scaffoldmaker/pull/177) ([mlin865](https://github.com/mlin865))
- Update the brainstem branch due to previous mapclient update [\176](https://github.com/ABI-Software/scaffoldmaker/pull/176) ([arti-sukasem](https://github.com/arti-sukasem))
- Update the pig lung branch due to previous mapclient update [\175](https://github.com/ABI-Software/scaffoldmaker/pull/175) ([arti-sukasem](https://github.com/arti-sukasem))
- Add shell layers [\173](https://github.com/ABI-Software/scaffoldmaker/pull/173) ([elias-soltani](https://github.com/elias-soltani))
- Update terms following discussion with SAWG [\172](https://github.com/ABI-Software/scaffoldmaker/pull/172) ([mlin865](https://github.com/mlin865))
[v0.3.0](https://github.com/ABI-Software/scaffoldmaker/tree/v0.3.0) (2021-11-23)
[Full Changelog](https://github.com/ABI-Software/scaffoldmaker/compare/v0.2.0...v0.3.0)
**Merged pull requests:**
- Stomach layers [\168](https://github.com/ABI-Software/scaffoldmaker/pull/168) ([mlin865](https://github.com/mlin865))
- Shield/sphere [\156](https://github.com/ABI-Software/scaffoldmaker/pull/156) ([elias-soltani](https://github.com/elias-soltani))
[v0.2.0](https://github.com/ABI-Software/scaffoldmaker/tree/v0.2.0) (2021-11-04)
[Full Changelog](https://github.com/ABI-Software/scaffoldmaker/compare/adb60ce6b19ea53e8ebbe03280e219e33f8cdfa9...v0.2.0)
**Implemented enhancements:**
- Add refinement to low order elements [\6](https://github.com/ABI-Software/scaffoldmaker/issues/6)
**Fixed bugs:**
- Scaffoldmaker import error Python 2 [\14](https://github.com/ABI-Software/scaffoldmaker/issues/14)
**Closed issues:**
- AttributeError: 'ScaffoldPackage' object has no attribute 'deepcopy' [\95](https://github.com/ABI-Software/scaffoldmaker/issues/95)
- Edit 'data\_coordinates' field for fiducial points [\53](https://github.com/ABI-Software/scaffoldmaker/issues/53)
- Add helper methods to scale scaffold [\27](https://github.com/ABI-Software/scaffoldmaker/issues/27)
**Merged pull requests:**
- Optimise imports and perform some PEP8 fixes. [\165](https://github.com/ABI-Software/scaffoldmaker/pull/165) ([hsorby](https://github.com/hsorby))
- opencmiss.maths fixes [\162](https://github.com/ABI-Software/scaffoldmaker/pull/162) ([rchristie](https://github.com/rchristie))
- Update inner surface of colonic mucosa with edits from SAWG [\161](https://github.com/ABI-Software/scaffoldmaker/pull/161) ([mlin865](https://github.com/mlin865))
- Add ILX for inner surface of colonic mucosa [\160](https://github.com/ABI-Software/scaffoldmaker/pull/160) ([mlin865](https://github.com/mlin865))
- Colon coordinates [\157](https://github.com/ABI-Software/scaffoldmaker/pull/157) ([mlin865](https://github.com/mlin865))
- Add parameter sets for mouse and pig bladder [\153](https://github.com/ABI-Software/scaffoldmaker/pull/153) ([keeran97](https://github.com/keeran97))
- Update bladder terms [\152](https://github.com/ABI-Software/scaffoldmaker/pull/152) ([elias-soltani](https://github.com/elias-soltani))
- Flat stomach [\151](https://github.com/ABI-Software/scaffoldmaker/pull/151) ([mlin865](https://github.com/mlin865))
- Mouse brainstem [\149](https://github.com/ABI-Software/scaffoldmaker/pull/149) ([arti-sukasem](https://github.com/arti-sukasem))
- Bladder ilx [\148](https://github.com/ABI-Software/scaffoldmaker/pull/148) ([zekh167](https://github.com/zekh167))
- Increment version number [\147](https://github.com/ABI-Software/scaffoldmaker/pull/147) ([rchristie](https://github.com/rchristie))
- Created parameters for rat and human [\146](https://github.com/ABI-Software/scaffoldmaker/pull/146) ([arti-sukasem](https://github.com/arti-sukasem))
- Embed organ landmarks [\145](https://github.com/ABI-Software/scaffoldmaker/pull/145) ([elias-soltani](https://github.com/elias-soltani))
- Updated mouse parameters and ILX for lung terms [\144](https://github.com/ABI-Software/scaffoldmaker/pull/144) ([arti-sukasem](https://github.com/arti-sukasem))
- added laterodorsal tip of the middle lobe to rat and mouse mesh [\143](https://github.com/ABI-Software/scaffoldmaker/pull/143) ([arti-sukasem](https://github.com/arti-sukasem))
- Remove ZincPythonTools dependency [\142](https://github.com/ABI-Software/scaffoldmaker/pull/142) ([rchristie](https://github.com/rchristie))
- Fix tests [\141](https://github.com/ABI-Software/scaffoldmaker/pull/141) ([rchristie](https://github.com/rchristie))
- Heart terms [\140](https://github.com/ABI-Software/scaffoldmaker/pull/140) ([rchristie](https://github.com/rchristie))
- Added Rat lung mesh parameters [\139](https://github.com/ABI-Software/scaffoldmaker/pull/139) ([arti-sukasem](https://github.com/arti-sukasem))
- added marker points for both human and mouse, updated mouse parameter… [\138](https://github.com/ABI-Software/scaffoldmaker/pull/138) ([arti-sukasem](https://github.com/arti-sukasem))
- Human bladder [\137](https://github.com/ABI-Software/scaffoldmaker/pull/137) ([zekh167](https://github.com/zekh167))
- created lung fissure annotation [\135](https://github.com/ABI-Software/scaffoldmaker/pull/135) ([arti-sukasem](https://github.com/arti-sukasem))
- Left atria PV annulus changes [\133](https://github.com/ABI-Software/scaffoldmaker/pull/133) ([rchristie](https://github.com/rchristie))
- Stomach [\132](https://github.com/ABI-Software/scaffoldmaker/pull/132) ([mlin865](https://github.com/mlin865))
- Brainstem [\128](https://github.com/ABI-Software/scaffoldmaker/pull/128) ([s-fong](https://github.com/s-fong))
- Fix annulus start/end mapping [\127](https://github.com/ABI-Software/scaffoldmaker/pull/127) ([rchristie](https://github.com/rchristie))
- Fix unused scale factor bugs [\126](https://github.com/ABI-Software/scaffoldmaker/pull/126) ([rchristie](https://github.com/rchristie))
- Added four fiducial points. [\125](https://github.com/ABI-Software/scaffoldmaker/pull/125) ([zekh167](https://github.com/zekh167))
- Bodycoordinates [\123](https://github.com/ABI-Software/scaffoldmaker/pull/123) ([elias-soltani](https://github.com/elias-soltani))
- Bifurcation tree start [\121](https://github.com/ABI-Software/scaffoldmaker/pull/121) ([rchristie](https://github.com/rchristie))
- Bladder dorsal ventral [\120](https://github.com/ABI-Software/scaffoldmaker/pull/120) ([zekh167](https://github.com/zekh167))
- Cattle intestines [\119](https://github.com/ABI-Software/scaffoldmaker/pull/119) ([mlin865](https://github.com/mlin865))
- Right and accessory lungs [\118](https://github.com/ABI-Software/scaffoldmaker/pull/118) ([arti-sukasem](https://github.com/arti-sukasem))
- Cylinder/circular core [\116](https://github.com/ABI-Software/scaffoldmaker/pull/116) ([elias-soltani](https://github.com/elias-soltani))
- Sharpen anterior edges of left and right human lungs [\115](https://github.com/ABI-Software/scaffoldmaker/pull/115) ([arti-sukasem](https://github.com/arti-sukasem))
- Added left lung parameters. [\114](https://github.com/ABI-Software/scaffoldmaker/pull/114) ([zekh167](https://github.com/zekh167))
- Right lung in a human [\113](https://github.com/ABI-Software/scaffoldmaker/pull/113) ([arti-sukasem](https://github.com/arti-sukasem))
- Fix boundary derivative smoothing [\112](https://github.com/ABI-Software/scaffoldmaker/pull/112) ([rchristie](https://github.com/rchristie))
- Cylinder/rim [\111](https://github.com/ABI-Software/scaffoldmaker/pull/111) ([elias-soltani](https://github.com/elias-soltani))
- Smooth derivative directions, add function options [\110](https://github.com/ABI-Software/scaffoldmaker/pull/110) ([rchristie](https://github.com/rchristie))
- Wedge [\109](https://github.com/ABI-Software/scaffoldmaker/pull/109) ([mlin865](https://github.com/mlin865))
- Bladder updated [\108](https://github.com/ABI-Software/scaffoldmaker/pull/108) ([zekh167](https://github.com/zekh167))
- Set fitted human lung parameters [\107](https://github.com/ABI-Software/scaffoldmaker/pull/107) ([rchristie](https://github.com/rchristie))
- Global field derivative smoothing [\106](https://github.com/ABI-Software/scaffoldmaker/pull/106) ([rchristie](https://github.com/rchristie))
- Update both lower and upper lobes in the left human. [\105](https://github.com/ABI-Software/scaffoldmaker/pull/105) ([arti-sukasem](https://github.com/arti-sukasem))
- Fix atria shape distortions [\104](https://github.com/ABI-Software/scaffoldmaker/pull/104) ([rchristie](https://github.com/rchristie))
- Add human lung lower lobe [\103](https://github.com/ABI-Software/scaffoldmaker/pull/103) ([arti-sukasem](https://github.com/arti-sukasem))
- Add mesh refinement to lung [\102](https://github.com/ABI-Software/scaffoldmaker/pull/102) ([rchristie](https://github.com/rchristie))
- Lungs [\101](https://github.com/ABI-Software/scaffoldmaker/pull/101) ([zekh167](https://github.com/zekh167))
- Rescale derivatives for annulus mesh [\100](https://github.com/ABI-Software/scaffoldmaker/pull/100) ([mlin865](https://github.com/mlin865))
- Parameter sets [\99](https://github.com/ABI-Software/scaffoldmaker/pull/99) ([s-fong](https://github.com/s-fong))
- Fix 1 element smoothing [\98](https://github.com/ABI-Software/scaffoldmaker/pull/98) ([rchristie](https://github.com/rchristie))
- Add path smooth cross derivatives function [\97](https://github.com/ABI-Software/scaffoldmaker/pull/97) ([rchristie](https://github.com/rchristie))
- Fix ScaffoldPackage deepcopy and meshedits [\96](https://github.com/ABI-Software/scaffoldmaker/pull/96) ([rchristie](https://github.com/rchristie))
- Cylinder/central path [\94](https://github.com/ABI-Software/scaffoldmaker/pull/94) ([elias-soltani](https://github.com/elias-soltani))
- Path1/sidederivatives [\93](https://github.com/ABI-Software/scaffoldmaker/pull/93) ([elias-soltani](https://github.com/elias-soltani))
- Annotation [\92](https://github.com/ABI-Software/scaffoldmaker/pull/92) ([s-fong](https://github.com/s-fong))
- Add scaffold interactive functions [\91](https://github.com/ABI-Software/scaffoldmaker/pull/91) ([rchristie](https://github.com/rchristie))
- Add subelements to user annotation groups [\90](https://github.com/ABI-Software/scaffoldmaker/pull/90) ([rchristie](https://github.com/rchristie))
- Stellate [\89](https://github.com/ABI-Software/scaffoldmaker/pull/89) ([s-fong](https://github.com/s-fong))
- Add functions to update user annotation groups [\88](https://github.com/ABI-Software/scaffoldmaker/pull/88) ([rchristie](https://github.com/rchristie))
- Annotation fix [\87](https://github.com/ABI-Software/scaffoldmaker/pull/87) ([rchristie](https://github.com/rchristie))
- Generalised cylinder [\86](https://github.com/ABI-Software/scaffoldmaker/pull/86) ([elias-soltani](https://github.com/elias-soltani))
- Bladder urethra [\85](https://github.com/ABI-Software/scaffoldmaker/pull/85) ([zekh167](https://github.com/zekh167))
- Add user-defined annotation groups [\83](https://github.com/ABI-Software/scaffoldmaker/pull/83) ([rchristie](https://github.com/rchristie))
- Fix 2D VTK export [\82](https://github.com/ABI-Software/scaffoldmaker/pull/82) ([rchristie](https://github.com/rchristie))
- Heart ventricles 3 and arterial valves [\81](https://github.com/ABI-Software/scaffoldmaker/pull/81) ([rchristie](https://github.com/rchristie))
- Multiple annotation groups [\80](https://github.com/ABI-Software/scaffoldmaker/pull/80) ([mlin865](https://github.com/mlin865))
- Pig colon [\79](https://github.com/ABI-Software/scaffoldmaker/pull/79) ([mlin865](https://github.com/mlin865))
- Bifurcation tree and tube fork [\78](https://github.com/ABI-Software/scaffoldmaker/pull/78) ([rchristie](https://github.com/rchristie))
- Fix heart test, opencmiss.utils version [\77](https://github.com/ABI-Software/scaffoldmaker/pull/77) ([rchristie](https://github.com/rchristie))
- Cecum [\76](https://github.com/ABI-Software/scaffoldmaker/pull/76) ([mlin865](https://github.com/mlin865))
- Improve rat heart after scale fix [\75](https://github.com/ABI-Software/scaffoldmaker/pull/75) ([rchristie](https://github.com/rchristie))
- Improve rat heart [\74](https://github.com/ABI-Software/scaffoldmaker/pull/74) ([rchristie](https://github.com/rchristie))
- Remove auricles from atria groups [\73](https://github.com/ABI-Software/scaffoldmaker/pull/73) ([rchristie](https://github.com/rchristie))
- Bladder annotation [\72](https://github.com/ABI-Software/scaffoldmaker/pull/72) ([zekh167](https://github.com/zekh167))
- Transformations in ScaffoldPackage [\71](https://github.com/ABI-Software/scaffoldmaker/pull/71) ([rchristie](https://github.com/rchristie))
- Improve annotations, refinement and VTK export [\70](https://github.com/ABI-Software/scaffoldmaker/pull/70) ([rchristie](https://github.com/rchristie))
- Implement phase [\68](https://github.com/ABI-Software/scaffoldmaker/pull/68) ([mlin865](https://github.com/mlin865))
- projection has been done [\67](https://github.com/ABI-Software/scaffoldmaker/pull/67) ([zekh167](https://github.com/zekh167))
- Improve annotation groups [\66](https://github.com/ABI-Software/scaffoldmaker/pull/66) ([rchristie](https://github.com/rchristie))
- removed indentation for lines of unittest [\65](https://github.com/ABI-Software/scaffoldmaker/pull/65) ([zekh167](https://github.com/zekh167))
- Move most zinc\_utils to opencmiss.utils [\64](https://github.com/ABI-Software/scaffoldmaker/pull/64) ([rchristie](https://github.com/rchristie))
- Small intestine scaffold [\63](https://github.com/ABI-Software/scaffoldmaker/pull/63) ([mlin865](https://github.com/mlin865))
- Bladder scaffold [\62](https://github.com/ABI-Software/scaffoldmaker/pull/62) ([zekh167](https://github.com/zekh167))
- Tests for colon and colon segment meshtypes [\61](https://github.com/ABI-Software/scaffoldmaker/pull/61) ([mlin865](https://github.com/mlin865))
- Put source under src folder, add test [\60](https://github.com/ABI-Software/scaffoldmaker/pull/60) ([rchristie](https://github.com/rchristie))
- Vary inner radius and tenia coli width along colon length [\59](https://github.com/ABI-Software/scaffoldmaker/pull/59) ([mlin865](https://github.com/mlin865))
- Serialise bytes string to JSON [\58](https://github.com/ABI-Software/scaffoldmaker/pull/58) ([rchristie](https://github.com/rchristie))
- Rename data fields to fiducial [\57](https://github.com/ABI-Software/scaffoldmaker/pull/57) ([rchristie](https://github.com/rchristie))
- Replace heart atria, improve parameters for all species [\56](https://github.com/ABI-Software/scaffoldmaker/pull/56) ([rchristie](https://github.com/rchristie))
- Pig colon [\55](https://github.com/ABI-Software/scaffoldmaker/pull/55) ([mlin865](https://github.com/mlin865))
- Mouse colon [\54](https://github.com/ABI-Software/scaffoldmaker/pull/54) ([mlin865](https://github.com/mlin865))
- Parameters for human 1 and 2 [\52](https://github.com/ABI-Software/scaffoldmaker/pull/52) ([mlin865](https://github.com/mlin865))
- Add single/double ostium scaffold [\51](https://github.com/ABI-Software/scaffoldmaker/pull/51) ([rchristie](https://github.com/rchristie))
- Implement cross-axis [\50](https://github.com/ABI-Software/scaffoldmaker/pull/50) ([mlin865](https://github.com/mlin865))
- Scale d2 along mesh with curvature of central line [\49](https://github.com/ABI-Software/scaffoldmaker/pull/49) ([mlin865](https://github.com/mlin865))
- Tenia coli [\48](https://github.com/ABI-Software/scaffoldmaker/pull/48) ([mlin865](https://github.com/mlin865))
- Add sub-scaffolds [\47](https://github.com/ABI-Software/scaffoldmaker/pull/47) ([rchristie](https://github.com/rchristie))
- Texture coordinates [\46](https://github.com/ABI-Software/scaffoldmaker/pull/46) ([mlin865](https://github.com/mlin865))
- Add rat, mouse heart parameters [\45](https://github.com/ABI-Software/scaffoldmaker/pull/45) ([rchristie](https://github.com/rchristie))
- Revisions based on comments from Colon Pull request \43 [\44](https://github.com/ABI-Software/scaffoldmaker/pull/44) ([mlin865](https://github.com/mlin865))
- Remove files that are no longer needed and update instruction. [\42](https://github.com/ABI-Software/scaffoldmaker/pull/42) ([alan-wu](https://github.com/alan-wu))
- Add scipy and numpy to required packages and change ZincPythonTools a… [\41](https://github.com/ABI-Software/scaffoldmaker/pull/41) ([alan-wu](https://github.com/alan-wu))
- Improve convergence when finding xi from arc distance [\40](https://github.com/ABI-Software/scaffoldmaker/pull/40) ([rchristie](https://github.com/rchristie))
- Support multiple parameter sets, add scaffold base class [\38](https://github.com/ABI-Software/scaffoldmaker/pull/38) ([rchristie](https://github.com/rchristie))
- Improved compatibility with python 2.7 [\37](https://github.com/ABI-Software/scaffoldmaker/pull/37) ([fowlkes](https://github.com/fowlkes))
- Allow 1 or 2 left and right pulmonary veins [\36](https://github.com/ABI-Software/scaffoldmaker/pull/36) ([rchristie](https://github.com/rchristie))
- Function for exporting scaffolds to vtk [\35](https://github.com/ABI-Software/scaffoldmaker/pull/35) ([rchristie](https://github.com/rchristie))
- Human stomach [\34](https://github.com/ABI-Software/scaffoldmaker/pull/34) ([rchristie](https://github.com/rchristie))
- Add cusps to heart arterial root [\33](https://github.com/ABI-Software/scaffoldmaker/pull/33) ([rchristie](https://github.com/rchristie))
- Partial arterial root [\32](https://github.com/ABI-Software/scaffoldmaker/pull/32) ([rchristie](https://github.com/rchristie))
- Add unit scale parameter [\31](https://github.com/ABI-Software/scaffoldmaker/pull/31) ([rchristie](https://github.com/rchristie))
- Add heart fiducial marker annotation points [\30](https://github.com/ABI-Software/scaffoldmaker/pull/30) ([rchristie](https://github.com/rchristie))
- Add new heart1 scaffold [\29](https://github.com/ABI-Software/scaffoldmaker/pull/29) ([rchristie](https://github.com/rchristie))
- Central line tube mesh [\28](https://github.com/ABI-Software/scaffoldmaker/pull/28) ([mlin865](https://github.com/mlin865))
- Add choice of arithmetic or harmonic mean derivatives [\26](https://github.com/ABI-Software/scaffoldmaker/pull/26) ([rchristie](https://github.com/rchristie))
- Separate variable interpolation from cubic sampling [\25](https://github.com/ABI-Software/scaffoldmaker/pull/25) ([rchristie](https://github.com/rchristie))
- Add new heartventricles1 scaffold [\24](https://github.com/ABI-Software/scaffoldmaker/pull/24) ([rchristie](https://github.com/rchristie))
- Linear basis through wall for sphere shell [\23](https://github.com/ABI-Software/scaffoldmaker/pull/23) ([mlin865](https://github.com/mlin865))
- Rename Scaffoldmaker class for Python 2 import [\22](https://github.com/ABI-Software/scaffoldmaker/pull/22) ([rchristie](https://github.com/rchristie))
- Lens [\21](https://github.com/ABI-Software/scaffoldmaker/pull/21) ([mlin865](https://github.com/mlin865))
- Add new atria1 [\20](https://github.com/ABI-Software/scaffoldmaker/pull/20) ([rchristie](https://github.com/rchristie))
- 3D Human stomach [\19](https://github.com/ABI-Software/scaffoldmaker/pull/19) ([Jagirhussan](https://github.com/Jagirhussan))
- Fix defaults and limits for number of elements around and up [\18](https://github.com/ABI-Software/scaffoldmaker/pull/18) ([mlin865](https://github.com/mlin865))
- Add solid sphere scaffold [\17](https://github.com/ABI-Software/scaffoldmaker/pull/17) ([mlin865](https://github.com/mlin865))
- Add full heart merging ventricles, base and atria [\16](https://github.com/ABI-Software/scaffoldmaker/pull/16) ([rchristie](https://github.com/rchristie))
- Add atria 2 scaffold [\15](https://github.com/ABI-Software/scaffoldmaker/pull/15) ([rchristie](https://github.com/rchristie))
- Correctly simplify the installation process. [\13](https://github.com/ABI-Software/scaffoldmaker/pull/13) ([metatoaster](https://github.com/metatoaster))
- Add annotation groups for ventricles 2 [\12](https://github.com/ABI-Software/scaffoldmaker/pull/12) ([rchristie](https://github.com/rchristie))
- Reduce distortion at septum by right atria [\11](https://github.com/ABI-Software/scaffoldmaker/pull/11) ([rchristie](https://github.com/rchristie))
- Close ventriclesbase2 [\10](https://github.com/ABI-Software/scaffoldmaker/pull/10) ([rchristie](https://github.com/rchristie))
- Started ventricles base 2 [\9](https://github.com/ABI-Software/scaffoldmaker/pull/9) ([rchristie](https://github.com/rchristie))
- Add new ventricles2 scaffold [\8](https://github.com/ABI-Software/scaffoldmaker/pull/8) ([rchristie](https://github.com/rchristie))
- Add refinement to trilinear elements [\7](https://github.com/ABI-Software/scaffoldmaker/pull/7) ([rchristie](https://github.com/rchristie))
- Close atria, add outlets [\5](https://github.com/ABI-Software/scaffoldmaker/pull/5) ([rchristie](https://github.com/rchristie))
- Add Scaffoldmaker class, atria mesh [\4](https://github.com/ABI-Software/scaffoldmaker/pull/4) ([rchristie](https://github.com/rchristie))
- Comment out debug print statements [\3](https://github.com/ABI-Software/scaffoldmaker/pull/3) ([rchristie](https://github.com/rchristie))
- Improve default options for ventricles and base [\2](https://github.com/ABI-Software/scaffoldmaker/pull/2) ([rchristie](https://github.com/rchristie))
- Improve and complete heart base elements [\1](https://github.com/ABI-Software/scaffoldmaker/pull/1) ([rchristie](https://github.com/rchristie))
\* *This Changelog was automatically generated by [github_changelog_generator](https://github.com/github-changelog-generator/github-changelog-generator)*