diff --git a/CHANGELOG.rst b/CHANGELOG.rst index f867e5c..7d99df9 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -1,9 +1,55 @@ Changelog ========= +Version 0.1.4 +------------- + +Density placement: Force scaling on voxels that are not full. Fix #27. (#28) + +split_into_halves existed in atlas_commons; remove the copy here (#26) + +Restrict ISH slice positions that are inside the volume_mask volume. (#25) + +Version 0.1.3 +------------- +Add excitatory split + +Version 0.1.2 +------------- + +Excitatory split (#19) + * Write SSCX layer-specific types to all isocortex + * Changed layer key in csv file, changed layer filter in metadata to make it specific for Isocortex layers, changed code to do isocortex instead of just SSCX + * made it isocortex specific + * Used code snippet from Dimitri to read in metadata and create layers + +Version 0.1.1 +------------- + +Update Roussel et al.'s pipeline to match implementation from the paper (#12) + * Update Roussel et al.'s pipeline to match the implementation from the paper. Htr3a is now split into vip and lamp5. + * Added a warning for the user in case the thresholding causes the dataset to be entirely null. + * A threshold can be applied to the Nissl and raw ISH datasets to remove a part of the background expression. + If the expression outside the test datasets is too high then the thresholding process will set the whole dataset to 0. Some tests will therefore randomly fail when this event happen. + +add examples to README.rst (#6) + * Add references to Rodarie's and Roussel's and Kim's paper. + * Add context for the AIBS datasets and pipeline steps. + * add note about memory usage + * Fix assertion errors due to float rounding issues for inhibitory neuron density optimization. + +Fixes to match previous pipeline + * Split mandatory ccfv2 fibers and cell containing regions combination from ccfv3 / ccfv2 annotation combination + * Add normalization and cell overlapping of Nissl and ISH dataset to match Erö's pipeline. + * Fix glia cell density placement, prevent negative densities. + * Add purely inhibitory regions for Erö's method to match model from 2019. + * Fix masks for cerebellar cortex, molecular and cortex L1 and related test. + + +fix warnings/deprecations (#5) + Version 0.1.0 ------------- -- Initial commit: extracts `densities`, `combination` and related tests from `nse/atlas-building-tools` [`NSETM_1685_`] .. _`NSETM-1685`: https://bbpteam.epfl.ch/project/issues/browse/NSETM-1685