small-fish-gui 2.0.1__py3-none-any.whl → 2.0.2__py3-none-any.whl

small_fish_gui/README.md

@@ -45,6 +45,9 @@ Spot detection is performed via *big-fish* a python implementation of FishQuant
 Analysis can be performed either fully interactively throught a Napari interface or performed automatically through a batch processing allowing for reproducible quantifications. 
 
 ## Installation
+
+### General setup
+
 If you don't have a python installation yet I would recommend the [miniconda distribution](https://docs.anaconda.com/free/miniconda/miniconda-other-installer-links/).
 
 It is higly recommanded to create a specific [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [virtual](https://docs.python.org/3.6/library/venv.html) environnement to install small fish.
@@ -57,13 +60,23 @@ Then download the small_fish package :
 ```bash
 pip install small_fish_gui
 ```
-<b> (Recommended) </b> Results visualisation is achieved through *Napari* which you can install with :
+Results visualisation is achieved through *Napari* which you can install with :
 
 ```bash
 pip install napari[all]
 ```
 
-## Run Small fish
+### Setting up GPU
+As of Small Fish 2.0.1 it is **highly** recommanded to set up GPU with cellpose since its new model, CellposeSAM, is very heavy computationally even more when attempting 3D segmentation.  
+First of all, try to run small fish gpu without additional commands depending on your configuration it could work straight out of the box. If encoutering any issue try first the following :
+
+```bash
+pip install --index-url https://download.pytorch.org/whl/cu124 torch torchvision torchaudio
+```
+
+If running into additional problems please look at [cellpose documentation](https://cellpose.readthedocs.io/en/latest/installation.html). 
+
+### Run Small fish
 
 First activate your python environnement : 
 ```bash

small_fish_gui/__init__.py

@@ -37,8 +37,14 @@ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 """
-__version__ = "2.0.1"
+__version__ = "2.0.2"
 __wiki__ = "https://github.com/2Echoes/small_fish_gui/wiki"
 
-import os
-os.environ["QT_QPA_PLATFORM"] = "xcb"
+import os, platform
+system_type = platform.system()
+
+if system_type == "Linux" :
+  try :
+    os.environ["QT_QPA_PLATFORM"] = "xcb"
+  except Exception :
+    pass

{small_fish_gui-2.0.1.dist-info → small_fish_gui-2.0.2.dist-info}/METADATA

@@ -1,10 +1,10 @@
 Metadata-Version: 2.4
 Name: small_fish_gui
-Version: 2.0.1
+Version: 2.0.2
 Summary: Small Fish is a python application for the analysis of smFish images. It provides a ready to use graphical interface to combine famous python packages for cell analysis without any need for coding.
-Project-URL: Homepage, https://github.com/SmallFishGUI/small_fish
+Project-URL: Homepage, https://github.com/SmallFishGUI/small_fish_gui
 Project-URL: Wiki, https://github.com/SmallFishGUI/small_fish_gui/wiki
-Project-URL: Issues, https://github.com/SmallFishGUI/small_fish/issues
+Project-URL: Issues, https://github.com/SmallFishGUI/small_fish_gui/issues
 Author-email: Slimani Floric <floric.slimani@live.com>
 License-File: LICENSE
 Classifier: License :: OSI Approved :: BSD License

{small_fish_gui-2.0.1.dist-info → small_fish_gui-2.0.2.dist-info}/RECORD

@@ -1,6 +1,6 @@
 small_fish_gui/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
-small_fish_gui/README.md,sha256=L_cbKyeAcWpMNqUe1fbMi0I0CqXbdN7kvPlCrLnOCF4,3736
-small_fish_gui/__init__.py,sha256=zd6tWcL3jZ69_S-j99FJggZqvQhB7yYUrWq0So8z3-c,2049
+small_fish_gui/README.md,sha256=fbqy1u3iUYNn_zvfHqRIhI2SHVaM2DSEovVo_CQlXTE,4378
+small_fish_gui/__init__.py,sha256=WNInvg3HaKrfuEOQHmnnZ5SoI-5o3EFgapeiX0rbzqo,2162
 small_fish_gui/__main__.py,sha256=xwpFMDuo0kkYvPamyhlTHJ68bymDfbRpPzKy3SKwezY,1639
 small_fish_gui/default_values.py,sha256=E5eoCIyIgaA18WcD5EAUrbKoEXoEEEk6ml3JPvFd_GI,921
 small_fish_gui/hints.py,sha256=q8G9ZbV-y7EUyOa8MjCTJltu750EvhGCalAU8INzeoo,2703
@@ -53,7 +53,7 @@ small_fish_gui/pipeline/spots.py,sha256=6yHpC_BkA42ZXRNyZ8qB49uhEhOIXYDUPU1Vy6aO
 small_fish_gui/pipeline/test.py,sha256=w4ZMGDmUDXxVgWTlZ2TKw19W8q5gcE9gLMKe0SWnRrw,2827
 small_fish_gui/pipeline/testing.ipynb,sha256=zIjnWwsqCBUqydvFx3n4R3_SlrBSwgWjDt50zn4SNgI,339174
 small_fish_gui/pipeline/utils.py,sha256=run6qtqCAe_mFnE3o1CnmF1xBBmK3ydgc8-jOV9P-_w,448
-small_fish_gui-2.0.1.dist-info/METADATA,sha256=7IktqcVTIaNQrJpJN9N6GwDRRAFFlrPJ2GRCyBxNQY8,2678
-small_fish_gui-2.0.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-small_fish_gui-2.0.1.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
-small_fish_gui-2.0.1.dist-info/RECORD,,
+small_fish_gui-2.0.2.dist-info/METADATA,sha256=IlYOrnIur72CdNHkwPeVW162UkUqS-e9HWqFJvvI-jU,2686
+small_fish_gui-2.0.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+small_fish_gui-2.0.2.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
+small_fish_gui-2.0.2.dist-info/RECORD,,